Discussion:
[gmx-users] Methanol SOL :Number of solvent molecules = 0
sharada
2007-12-10 10:30:46 UTC
Permalink
Dear Gramacs users,
I am trying to simulate a peptide in Methanol. I am using Methanol216.gro file for the solvent. I could create the proper top and gro files of the peptide with the methanol solvent. However at the genbox step it says Number of solvent molecules =0
but when I open the final .gro file it has solvent molecules. Whereas the .top file does not contain the solvent molecules.
I am inserting the output of genbox and .gro file for information.
genbox -cp agg2box.gro -cs methanol216.gro -o agg2_b4em.gro -p agg2.top
Reading solute configuration
GROwing Monsters And Cloning Shrimps
Containing 71 atoms in 6 residues
Initialising van der waals distances...
Reading solvent configuration
"Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
MeOH ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 3042 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Neighborsearching with a cut-off of 0.45
Grid: 14 x 15 x 13 cells
Succesfully made neighbourlist
nri = 9007, nrj = 188363
Checking Protein-Solvent overlap: tested 693 pairs, removed 63 atoms.
Checking Solvent-Solvent overlap: tested 11134 pairs, removed 513 atoms.
Added 522 molecules
Generated solvent containing 1566 atoms in 522 residues
Writing generated configuration to agg2_b4em.gro
Back Off! I just backed up agg2_b4em.gro to ./#agg2_b4em.gro.1#
GROwing Monsters And Cloning Shrimps
Output configuration contains 1637 atoms in 528 residues
Volume : 35.0595 (nm^3)
Density : 752.963 (g/l)
Number of SOL molecules: 0
Processing topology
Back Off! I just backed up agg2.top to ./#agg2.top.1#
-----------------------------------------------------------------------------------------------------------------------------
agg2_b4em.gro file reads like this......
GROwing Monsters And Cloning Shrimps
1637
1VAL N 1 0.990 1.146 1.482
1VAL H1 2 0.961 1.053 1.507
1VAL H2 3 0.926 1.212 1.519
1VAL H3 4 0.994 1.154 1.382
1VAL CA 5 1.126 1.172 1.539
1VAL CB 6 1.229 1.061 1.497
1VAL CG1 7 1.372 1.085 1.552
1VAL CG2 8 1.189 0.918 1.542
1VAL C 9 1.170 1.317 1.498
1VAL O 10 1.202 1.344 1.382
2GLN N 11 1.175 1.411 1.595
2GLN H 12 1.145 1.386 1.687
2GLN CA 13 1.223 1.549 1.570
2GLN CB 14 1.153 1.643 1.673
2GLN CG 15 1.175 1.794 1.647
2GLN CD 16 1.115 1.887 1.752
2GLN OE1 17 1.180 1.929 1.847
2GLN NE2 18 0.990 1.924 1.740
2GLN HE21 19 0.936 1.892 1.662
2GLN HE22 20 0.949 1.985 1.808
2GLN C 21 1.379 1.558 1.572
---------
----------
- -------
526MeOH Me1 1629 2.760 3.368 2.738
526MeOH O2 1630 2.695 3.423 2.632
526MeOH H3 1631 2.615 3.371 2.606
527MeOH Me1 1632 0.288 3.224 2.925
527MeOH O2 1633 0.194 3.156 2.996
527MeOH H3 1634 0.212 3.059 2.983
528MeOH Me1 1635 2.506 3.095 2.599
528MeOH O2 1636 2.457 3.218 2.567
528MeOH H3 1637 2.390 3.204 2.494
3.30500 3.58500 2.95900
Why does it say there are no SOL molecules. Where exactly am I going wrong ?
Kindly advice me. Thankyou for your patience.
sharada
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Justin A. Lemkul
2007-12-10 11:36:56 UTC
Permalink
Post by sharada
Dear Gramacs users,
I am trying to simulate a peptide in Methanol. I am using Methanol216.gro
file for the solvent. I could create the proper top and gro files of the
peptide with the methanol solvent. However at the genbox step it says Number
of solvent molecules =0
but when I open the final .gro file it has solvent molecules. Whereas the
.top file does not contain the solvent molecules.
I am inserting the output of genbox and .gro file for information.
genbox -cp agg2box.gro -cs methanol216.gro -o agg2_b4em.gro -p agg2.top
Reading solute configuration
GROwing Monsters And Cloning Shrimps
Containing 71 atoms in 6 residues
Initialising van der waals distances...
Reading solvent configuration
"Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
MeOH ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 3042 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Neighborsearching with a cut-off of 0.45
Grid: 14 x 15 x 13 cells
Succesfully made neighbourlist
nri = 9007, nrj = 188363
Checking Protein-Solvent overlap: tested 693 pairs, removed 63 atoms.
Checking Solvent-Solvent overlap: tested 11134 pairs, removed 513 atoms.
Added 522 molecules
Generated solvent containing 1566 atoms in 522 residues
Writing generated configuration to agg2_b4em.gro
Back Off! I just backed up agg2_b4em.gro to ./#agg2_b4em.gro.1#
GROwing Monsters And Cloning Shrimps
Output configuration contains 1637 atoms in 528 residues
Volume : 35.0595 (nm^3)
Density : 752.963 (g/l)
Number of SOL molecules: 0
Processing topology
Back Off! I just backed up agg2.top to ./#agg2.top.1#
-----------------------------------------------------------------------------------------------------------------------------
Post by sharada
agg2_b4em.gro file reads like this......
GROwing Monsters And Cloning Shrimps
1637
1VAL N 1 0.990 1.146 1.482
1VAL H1 2 0.961 1.053 1.507
1VAL H2 3 0.926 1.212 1.519
1VAL H3 4 0.994 1.154 1.382
1VAL CA 5 1.126 1.172 1.539
1VAL CB 6 1.229 1.061 1.497
1VAL CG1 7 1.372 1.085 1.552
1VAL CG2 8 1.189 0.918 1.542
1VAL C 9 1.170 1.317 1.498
1VAL O 10 1.202 1.344 1.382
2GLN N 11 1.175 1.411 1.595
2GLN H 12 1.145 1.386 1.687
2GLN CA 13 1.223 1.549 1.570
2GLN CB 14 1.153 1.643 1.673
2GLN CG 15 1.175 1.794 1.647
2GLN CD 16 1.115 1.887 1.752
2GLN OE1 17 1.180 1.929 1.847
2GLN NE2 18 0.990 1.924 1.740
2GLN HE21 19 0.936 1.892 1.662
2GLN HE22 20 0.949 1.985 1.808
2GLN C 21 1.379 1.558 1.572
---------
----------
- -------
526MeOH Me1 1629 2.760 3.368 2.738
526MeOH O2 1630 2.695 3.423 2.632
526MeOH H3 1631 2.615 3.371 2.606
527MeOH Me1 1632 0.288 3.224 2.925
527MeOH O2 1633 0.194 3.156 2.996
527MeOH H3 1634 0.212 3.059 2.983
528MeOH Me1 1635 2.506 3.095 2.599
528MeOH O2 1636 2.457 3.218 2.567
528MeOH H3 1637 2.390 3.204 2.494
3.30500 3.58500 2.95900
Why does it say there are no SOL molecules. Where exactly am I going wrong ?
Kindly advice me. Thankyou for your patience.
sharada
My guess would be that it is because there are no molecules named SOL in your
output. Gromacs uses SOL for water, and since your system lacks water, genbox
is accurately telling you there are no "SOL" within the output.

Note the line above where genbox is telling you that it added 522 molecules, and
add this information into your .top file.

-Justin


========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================
Xavier Periole
2007-12-10 23:13:34 UTC
Permalink
Note that topology of the methanol in the gromacs distribution does
not correspond to the original GROMOS methanol model. One distance
is changed and the original model does not have an angle discribing
CMET-OMET-H but a distance between CMET-H.

Anybody knows where the changes come from?

The bond topology of the original GROMOS model is as below.

[ bonds ]
; ai aj funct c0 c1
1 2 1 0.14300 376560.
2 3 1 0.10000 313800.
1 3 1 0.19880 313800.

XAvier.

On Mon, 10 Dec 2007 06:36:56 -0500
Post by sharada
Post by sharada
Dear Gramacs users,
I am trying to simulate a peptide in Methanol. I am using Methanol216.gro
file for the solvent. I could create the proper top and gro files of the
peptide with the methanol solvent. However at the genbox step it says Number
of solvent molecules =0
but when I open the final .gro file it has solvent molecules. Whereas the
.top file does not contain the solvent molecules.
I am inserting the output of genbox and .gro file for information.
genbox -cp agg2box.gro -cs methanol216.gro -o agg2_b4em.gro -p agg2.top
Reading solute configuration
GROwing Monsters And Cloning Shrimps
Containing 71 atoms in 6 residues
Initialising van der waals distances...
Reading solvent configuration
"Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
MeOH ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 3042 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Neighborsearching with a cut-off of 0.45
Grid: 14 x 15 x 13 cells
Succesfully made neighbourlist
nri = 9007, nrj = 188363
Checking Protein-Solvent overlap: tested 693 pairs, removed 63 atoms.
Checking Solvent-Solvent overlap: tested 11134 pairs, removed 513 atoms.
Added 522 molecules
Generated solvent containing 1566 atoms in 522 residues
Writing generated configuration to agg2_b4em.gro
Back Off! I just backed up agg2_b4em.gro to ./#agg2_b4em.gro.1#
GROwing Monsters And Cloning Shrimps
Output configuration contains 1637 atoms in 528 residues
Volume : 35.0595 (nm^3)
Density : 752.963 (g/l)
Number of SOL molecules: 0
Processing topology
Back Off! I just backed up agg2.top to ./#agg2.top.1#
-----------------------------------------------------------------------------------------------------------------------------
Post by sharada
agg2_b4em.gro file reads like this......
GROwing Monsters And Cloning Shrimps
1637
1VAL N 1 0.990 1.146 1.482
1VAL H1 2 0.961 1.053 1.507
1VAL H2 3 0.926 1.212 1.519
1VAL H3 4 0.994 1.154 1.382
1VAL CA 5 1.126 1.172 1.539
1VAL CB 6 1.229 1.061 1.497
1VAL CG1 7 1.372 1.085 1.552
1VAL CG2 8 1.189 0.918 1.542
1VAL C 9 1.170 1.317 1.498
1VAL O 10 1.202 1.344 1.382
2GLN N 11 1.175 1.411 1.595
2GLN H 12 1.145 1.386 1.687
2GLN CA 13 1.223 1.549 1.570
2GLN CB 14 1.153 1.643 1.673
2GLN CG 15 1.175 1.794 1.647
2GLN CD 16 1.115 1.887 1.752
2GLN OE1 17 1.180 1.929 1.847
2GLN NE2 18 0.990 1.924 1.740
2GLN HE21 19 0.936 1.892 1.662
2GLN HE22 20 0.949 1.985 1.808
2GLN C 21 1.379 1.558 1.572
---------
----------
- -------
526MeOH Me1 1629 2.760 3.368 2.738
526MeOH O2 1630 2.695 3.423 2.632
526MeOH H3 1631 2.615 3.371 2.606
527MeOH Me1 1632 0.288 3.224 2.925
527MeOH O2 1633 0.194 3.156 2.996
527MeOH H3 1634 0.212 3.059 2.983
528MeOH Me1 1635 2.506 3.095 2.599
528MeOH O2 1636 2.457 3.218 2.567
528MeOH H3 1637 2.390 3.204 2.494
3.30500 3.58500 2.95900
Why does it say there are no SOL molecules. Where exactly am I going wrong ?
Kindly advice me. Thankyou for your patience.
sharada
My guess would be that it is because there are no molecules named SOL in your
output. Gromacs uses SOL for water, and since your system lacks water, genbox
is accurately telling you there are no "SOL" within the output.
Note the line above where genbox is telling you that it added 522 molecules, and
add this information into your .top file.
-Justin
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
sharada
2007-12-11 05:29:12 UTC
Permalink
Dear Dr. Justin A. Lemkul
Thank you for your reply. I tried adding the line 'SOL 522 ' at the end of the .top file
but genbox is deleting the line.
------------------------------------------------------------
Output configuration contains 1076 atoms in 341 residues
Volume : 24.1334 (nm^3)
Density : 720.413 (g/l)
Number of SOL molecules: 0
Processing topology
Removing line #480 'SOL 522' from topology file (agg2.top)
-------------------------------------------------------------------------------------------
Thankyou Dr. Xavier Periole for indicating that the bonds and angle information does not match with the original Gromos distributed file. I am inserting methanol.itp file which came with gromacs distribution. I downloaded the methanol216.gro.gz from gromacs site. Should I change the bond values in the itp file? But it still does not solve the problem of 'SOL molecules'. Since .top file indicates "#include "spc.itp". So if I change it to #methanol.itp" it should work.
-----------------------------------------------
[root at ccmb top]# more methanol.itp
#ifndef _FF_GROMOS96
[ atomtypes ]
; type mass charge ptype c6 c12
OMET 15.999 -0.69 A 2.6169e-3 2.5231e-6
OW 15.999 -0.82 A 2.6170e-3 2.6330e-6
CMET 15.035 0.29 A 8.8758e-3 17.8426e-6
H 1.008 0.4 A 0.0 0.0
HW 1.008 0.41 A 0.0 0.0
#endif
[ moleculetype ]
; name nrexcl
Methanol 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
#ifdef _FF_GROMOS96
1 CMET 1 MeOH Me1 1 0.176 15.035
2 OMET 1 MeOH O2 1 -0.574 15.999
3 H 1 MeOH H3 1 0.398 1.008
#else
1 CMET 1 MeOH Me1 1 Regards
sharada 0.29 15.035
2 OMET 1 MeOH O2 1 -0.69 15.999
3 H 1 MeOH H3 1 0.40 1.008
#endif
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.13600 376560.
2 3 1 0.10000 313800.
[ angles ]
; ai aj ak funct c0 c1
1 2 3 1 108.53 397.5
Regards
sharada
(CCMB)
-------------------------------------------------------------------------------------------------------------------------------------------------
-- Original Message --
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Mon, 10 Dec 2007 06:36:56 -0500
Subject: Re: [gmx-users] Methanol SOL :Number of solvent molecules = 0
Post by sharada
526MeOH Me1 1629 2.760 3.368 2.738
526MeOH O2 1630 2.695 3.423 2.632
526MeOH H3 1631 2.615 3.371 2.606
527MeOH Me1 1632 0.288 3.224 2.925
527MeOH O2 1633 0.194 3.156 2.996
527MeOH H3 1634 0.212 3.059 2.983
528MeOH Me1 1635 2.506 3.095 2.599
528MeOH O2 1636 2.457 3.218 2.567
528MeOH H3 1637 2.390 3.204 2.494
3.30500 3.58500 2.95900
Why does it say there are no SOL molecules. Where exactly am I going wrong ?
Kindly advice me. Thankyou for your patience.
sharada
My guess would be that it is because there are no molecules named SOL in your
output. Gromacs uses SOL for water, and since your system lacks water, genbox
is accurately telling you there are no "SOL" within the output.
Note the line above where genbox is telling you that it added 522 molecules, and
add this information into your .top file.
-Justin
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




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Mark Abraham
2007-12-11 06:06:04 UTC
Permalink
Post by sharada
Dear Dr. Justin A. Lemkul
Thank you for your reply. I tried adding the line 'SOL 522 ' at the end
of the .top file
but genbox is deleting the line.
It will also need to correspond to a " [ molecule ] " section named SOL
and the residues in your gro file will need to be named SOL.
Post by sharada
------------------------------------------------------------
Output configuration contains 1076 atoms in 341 residues
Volume : 24.1334 (nm^3)
Density : 720.413 (g/l)
Number of SOL molecules: 0
Processing topology
Removing line #480 'SOL 522' from topology file (agg2.top)
-------------------------------------------------------------------------------------------
Thankyou Dr. Xavier Periole for indicating that the bonds and angle
information does not match with the original Gromos distributed file. I
am inserting methanol.itp file which came with gromacs distribution. I
downloaded the methanol216.gro.gz from gromacs site. Should I change
the bond values in the itp file? But it still does not solve the problem
of 'SOL molecules'. Since .top file indicates "#include "spc.itp". So if
I change it to #methanol.itp" it should work.
That might work, by achieving part of what I suggest above, but you'll
still need to change names in the .itp and .gro.
Post by sharada
-----------------------------------------------
[root at ccmb top]# more methanol.itp
Don't do daily work as root, unless you like pain.

Mark
sharada
2007-12-11 10:10:04 UTC
Permalink
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the #include line to "methanol.itp"
It now seemed to have written the solvent molecules in the top file with SOL as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am also attaching the .gro,.itp,.top files. for information. Did I miss out anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Cleaning up temporary file grompp5RBSRX
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1264
Fatal error:
No such moleculetype SOL
-------------------------------------------------------
I never prefer working in root as I know the problems. Thanks for suggesting. I needed to change the methanol.itp and methanol216.gro which could be possible only through root.
regards
sharada












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Xavier Periole
2007-12-11 11:07:27 UTC
Permalink
in your agg2t.top you should replace the last line :
SOL XXX
by:
Methanol XXX

which is the name of the molecule.

You should also remove the angle definition in methanol.itp. Placing
a ";" at the beginning of the line is enough.

XAvier

On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
Post by sharada
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the
#include line to "methanol.itp"
It now seemed to have written the solvent molecules in the top file with SOL
as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am
also attaching the .gro,.itp,.top files. for information. Did I miss out
anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Cleaning up temporary file grompp5RBSRX
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1264
No such moleculetype SOL
-------------------------------------------------------
I never prefer working in root as I know the problems. Thanks for
suggesting. I needed to change the methanol.itp and methanol216.gro which
could be possible only through root.
regards
sharada
-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
sharada
2007-12-11 12:24:33 UTC
Permalink
Dear Dr. Xavier Periole,
Thank you for guiding me through. I could solve the problem of setting up the system for minimization. However When started minimization run for 2000 steps with steepest descent , I encountered yet another problem. which is as follows ..
Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 2000
Grid: 4 x 5 x 4 cells
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Step Time Lambda
0 0.00000 0.00000
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
-------------------------------------------------------
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
Now where do I go from here? Its asking me to energy minimize the system which what I am trying to do ! What is this ci value and why is it so high? Kindly help me I am once again stuck.
regards
sharada

-- Original Message --
From: "Xavier Periole" <X.Periole at rug.nl>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 11 Dec 2007 12:07:27 +0100
Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules
= 0
in your agg2t.top you should replace the last line :
SOL XXX
by:
Methanol XXX
which is the name of the molecule.
You should also remove the angle definition in methanol.itp. Placing
a ";" at the beginning of the line is enough.
XAvier
On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
Post by sharada
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the
#include line to "methanol.itp"
It now seemed to have written the solvent molecules in the top file with SOL
as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am
also attaching the .gro,.itp,.top files. for information. Did I miss out
anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o
agg2_em.tpr
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Cleaning up temporary file grompp5RBSRX
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1264
No such moleculetype SOL
-------------------------------------------------------
I never prefer working in root as I know the problems. Thanks for
suggesting. I needed to change the methanol.itp and methanol216.gro which
could be possible only through root.
regards
sharada
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




-------------- next part --------------
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sharada
2007-12-12 12:04:36 UTC
Permalink
Dear Dr. Xavier Periole,
Thank you for guiding me through. I could solve the problem of setting up the system for minimization. However When started minimization run for 2000 steps with steepest descent , I encountered yet another problem. which is as follows ..
Methanol optimization:
Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 2000
Grid: 4 x 5 x 4 cells
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Step Time Lambda
0 0.00000 0.00000
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]
Please report this to the mailing list (gmx-users at gromacs.org)
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Now where do I go from here? Its asking me to energy minimize the system which is what I am trying to do ! What is this ci value and why is it so high? Kindly help me I am once again stuck. Furthermore, when I minimized the same peptide in SPC216 water box of 1108 water molecules for 2000 steps this error did not appear. When I compared the md.log files in both the cases I found that in case of water optimization of SPC water was enabled where as this line for methanol was missing which should mean that the energies are shooting off scale is that right ? Should I optimize my system in vacuo before simmulating in methanol?
Water optimization:
{Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 1108 molecules.
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 3396
Started Steepest Descents on node 0 Wed Dec 12 15:52:11 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 2000
Going to use C-settle (1108 waters)
wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Grid: 4 x 5 x 4 cells}
regards
sharada

-- Original Message --
From: "Xavier Periole" <X.Periole at rug.nl>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 11 Dec 2007 12:07:27 +0100
Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules
= 0
in your agg2t.top you should replace the last line :
SOL XXX
by:
Methanol XXX
which is the name of the molecule.
You should also remove the angle definition in methanol.itp. Placing
a ";" at the beginning of the line is enough.
XAvier
On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
Post by sharada
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the
#include line to "methanol.itp"
It now seemed to have written the solvent molecules in the top file with SOL
as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am
also attaching the .gro,.itp,.top files. for information. Did I miss out
anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o
agg2_em.tpr
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Cleaning up temporary file grompp5RBSRX
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1264
No such moleculetype SOL
-------------------------------------------------------
I never prefer working in root as I know the problems. Thanks for
suggesting. I needed to change the methanol.itp and methanol216.gro which
could be possible only through root.
regards
sharada
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



-------------- next part --------------
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Xavier Periole
2007-12-12 14:04:03 UTC
Permalink
Stop the minimization at 100 steps and then equilibrate. If the
problem persists check your topology.

XAvier
Post by sharada
Dear Dr. Xavier Periole,
Thank you for guiding me through. I could solve the problem of setting up
the system for minimization. However When started minimization run for 2000
steps with steepest descent , I encountered yet another problem. which is as
follows ..
Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
Removing pbc first time
Done rmpbc
Tolerance (Fmax) = 1.00000e+01
Number of steps = 2000
Grid: 4 x 5 x 4 cells
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Step Time Lambda
0 0.00000 0.00000
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]
Please report this to the mailing list (gmx-users at gromacs.org)
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Now where do I go from here? Its asking me to energy minimize the system
which is what I am trying to do ! What is this ci value and why is it so
high? Kindly help me I am once again stuck. Furthermore, when I minimized
the same peptide in SPC216 water box of 1108 water molecules for 2000 steps
this error did not appear. When I compared the md.log files in both the cases
I found that in case of water optimization of SPC water was enabled where as
this line for methanol was missing which should mean that the energies are
shooting off scale is that right ? Should I optimize my system in vacuo
before simmulating in methanol?
{Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 1108 molecules.
Initiating Steepest Descents
Center of mass motion removal mode is Linear
0: rest, initial mass: 3396
Started Steepest Descents on node 0 Wed Dec 12 15:52:11 2007
Removing pbc first time
Done rmpbc
Tolerance (Fmax) = 1.00000e+01
Number of steps = 2000
Going to use C-settle (1108 waters)
wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Grid: 4 x 5 x 4 cells}
regards
sharada
-- Original Message --
From: "Xavier Periole" <X.Periole at rug.nl>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 11 Dec 2007 12:07:27 +0100
Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules
= 0
SOL XXX
Methanol XXX
which is the name of the molecule.
You should also remove the angle definition in methanol.itp. Placing
a ";" at the beginning of the line is enough.
XAvier
On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
Post by sharada
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the
#include line to "methanol.itp"
It now seemed to have written the solvent molecules in the top file with SOL
as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am
also attaching the .gro,.itp,.top files. for information. Did I miss out
anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o
agg2_em.tpr
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Cleaning up temporary file grompp5RBSRX
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1264
No such moleculetype SOL
-------------------------------------------------------
I never prefer working in root as I know the problems. Thanks for
suggesting. I needed to change the methanol.itp and methanol216.gro which
could be possible only through root.
regards
sharada
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------

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