[gmx-users] Box generation for monoclinic crystal

Post by ramesh cheerla
Dear Gromacs users,
I am planing to simulate a polymeric
crystal in gromacs, which is of monoclinic unit cell with cell
parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4
deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction
'2' unit cells along 'b' direction and 4 unit cells along 'c' direction.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792
-angles 90 125.4 90
1) Am i using the editconf in correct manner for generation of box for
the monoclinic crystal, though the crystal is of monoclinic i am
using box type as triclinic
i haven't found any specific method for the generation of box for the
monoclinic crystal.
2) Is there any specific method to generate the box for the monoclinic
crystals.
3) The notations for the lattice parameters of the crystal i.e 'a' ,
'b' , 'c' and angles alpha, beta , gamma used by crystallography and
the gromacs editconf are the same or different, why because if i use
WARNING: Triclinic box is too skewed.

ramesh cheerla

2012-04-10 18:13:18 UTC

Dear Mark,

Thank you for reply, sorry for not being very clear, Here my
doubt is can i use triclinic box for the simulations of the crystal whose
unit cell is monoclinic. As i said earlier i have tried editconf as
editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792
-angles 90 125.4 90
it gave the following warning

WARNING: Triclinic box is too skewed.

for clarity here i am sending a part of the output file generated by the
editconf
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 -0.025 0.408 -0.045
1PEGA C2 2 -0.015 0.326 0.084
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.60800 6.35148 0.00000 0.00000 0.00000 0.00000
-4.51376 -0.00000
if i change the angles while using the editconf i observed the following
changes

editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792
-angles 90 90 125.4
in this case editconf haven't given any warning and the output as follows

God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 1.477 0.167 0.675
1PEGA C2 2 1.487 0.085 0.804
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077 0.00000
-0.00000 -0.00000

Can you please help me in this regard.

thank you in advance.

Post by ramesh cheerla
Dear Gromacs users,
I am planing to simulate a polymeric crystal in
gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm
b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424
type i.e 4 unit cells along 'a' direction '2' unit cells along 'b'
direction and 4 unit cells along 'c' direction.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792
-angles 90 125.4 90
1) Am i using the editconf in correct manner for generation of box for
the monoclinic crystal, though the crystal is of monoclinic i am using box
type as triclinic
i haven't found any specific method for the generation of box for the
monoclinic crystal.
2) Is there any specific method to generate the box for the monoclinic
crystals.
3) The notations for the lattice parameters of the crystal i.e 'a' , 'b'
, 'c' and angles alpha, beta , gamma used by crystallography and the
gromacs editconf are the same or different, why because if i use editconf
WARNING: Triclinic box is too skewed.

This means equation 3.3 of the manual is not true. Maybe beta should be
acute? I've no idea of necessity or convention here.
Inspecting the whole output of editconf is probably instructive, but
you've kept all that information to yourself instead of re-thinking how
your repeat post might be constructed so as to make it easier / more likely
for people help you. Likewise the final line of out_box.gro. Make sure you
have read and understood what documentation is available with editconf -h
and in manual section 3.2.
Mark
--
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Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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Tsjerk Wassenaar

2012-04-10 18:52:37 UTC

Hi Ramesh,

Maybe it is easier, and less error-prone, to work in PDB format,
specifying the box as a CRYST1 record. You can use the PDB format
anywhere in your workflow where GRO format is used.

Cheers,

Tsjerk

Post by ramesh cheerla
Dear Mark,
???????????? Thank you for reply, sorry for not being very clear, Here? my
doubt is can i use? triclinic box for the simulations of the crystal whose
unit cell is monoclinic. As i said earlier? i have tried editconf as
editconf -f input.gro -o out_box1.gro ?-bt triclinic -box 3.22 2.608 7.792
?-angles 90 ?125.4 90
it gave the following warning
WARNING: Triclinic box is too skewed.
for clarity here i am sending a part of the output file generated by the
editconf
God Rules Over Mankind, Animals, Cosmos and Such
?6528
??? 1PEGA??? C1??? 1? -0.025?? 0.408? -0.045
??? 1PEGA??? C2??? 2? -0.015?? 0.326?? 0.084
???? ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
???? 3.22000?? 2.60800?? 6.35148?? 0.00000?? 0.00000?? 0.00000?? 0.00000
-4.51376? -0.00000
if i change the angles while using the editconf i observed the following
changes
editconf -f input.gro -o out_box2.gro ?-bt triclinic -box 3.22 2.608 7.792
?-angles 90? 90 125.4
in this case editconf haven't given any warning and the output as follows
?God Rules Over Mankind, Animals, Cosmos and Such
?6528
??? 1PEGA??? C1??? 1?? 1.477?? 0.167?? 0.675
??? 1PEGA??? C2??? 2?? 1.487?? 0.085?? 0.804
???? ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
?? 3.22000?? 2.12585?? 7.79200?? 0.00000?? 0.00000? -1.51077?? 0.00000
-0.00000? -0.00000
Can you please help me in this regard.
thank you in advance.
On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham <Mark.Abraham at anu.edu.au>

Post by ramesh cheerla
Dear Gromacs users,
? ? ? ? ? ? ? ? ? ? ? ? ? I am planing to simulate a polymeric crystal in
gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm
b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424
type ?i.e 4 unit cells along 'a' direction ?'2' unit cells along 'b'
direction and 4 unit cells along 'c' direction.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
editconf -f input.gro -o out_box.gro ?-bt tric -box 3.22 2.608 7.792
?-angles 90 ?125.4 90
1) Am i using the editconf in correct manner for generation of box for
the monoclinic crystal, though the crystal is of monoclinic ?i am using box
type as triclinic
i haven't found any specific method for the generation of box for the
monoclinic crystal.
2) Is there any specific method to generate the box for the monoclinic
crystals.
3) The notations for the lattice parameters of the crystal i.e 'a' , 'b'
, 'c' and angles alpha, beta , gamma used by crystallography and the gromacs
editconf are the same or different, why because if i use editconf as above i
WARNING: Triclinic box is too skewed.

This means equation 3.3 of the manual is not true. Maybe beta should be
acute? I've no idea of necessity or convention here.
Inspecting the whole output of editconf is probably instructive, but
you've kept all that information to yourself instead of re-thinking how your
repeat post might be constructed so as to make it easier / more likely for
people help you. Likewise the final line of out_box.gro. Make sure you have
read and understood what documentation is available with editconf -h and in
manual section 3.2.
Mark
--
gmx-users mailing list ? ?gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
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--
gmx-users mailing list ? ?gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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ramesh cheerla

2012-04-10 20:17:03 UTC

Dear Tsjerk,

Thank you for your reply, I will try to work with PDB format and get back
to you.

Post by Tsjerk Wassenaar
Hi Ramesh,
Maybe it is easier, and less error-prone, to work in PDB format,
specifying the box as a CRYST1 record. You can use the PDB format
anywhere in your workflow where GRO format is used.
Cheers,
Tsjerk

Post by ramesh cheerla
Dear Mark,
Thank you for reply, sorry for not being very clear, Here

Post by ramesh cheerla
doubt is can i use triclinic box for the simulations of the crystal

whose

Post by ramesh cheerla
unit cell is monoclinic. As i said earlier i have tried editconf as
editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608

7.792

Post by ramesh cheerla
-angles 90 125.4 90
it gave the following warning
WARNING: Triclinic box is too skewed.
for clarity here i am sending a part of the output file generated by the
editconf
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 -0.025 0.408 -0.045
1PEGA C2 2 -0.015 0.326 0.084
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.60800 6.35148 0.00000 0.00000 0.00000 0.00000
-4.51376 -0.00000
if i change the angles while using the editconf i observed the following
changes
editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608

7.792

Post by ramesh cheerla
-angles 90 90 125.4
in this case editconf haven't given any warning and the output as follows
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 1.477 0.167 0.675
1PEGA C2 2 1.487 0.085 0.804
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077 0.00000
-0.00000 -0.00000
Can you please help me in this regard.
thank you in advance.
On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham <Mark.Abraham at anu.edu.au>

Post by ramesh cheerla
Dear Gromacs users,
I am planing to simulate a polymeric crystal

Post by ramesh cheerla
gromacs, which is of monoclinic unit cell with cell parameters a =

0.805 nm

Post by ramesh cheerla
b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of

424

Post by ramesh cheerla
type i.e 4 unit cells along 'a' direction '2' unit cells along 'b'
direction and 4 unit cells along 'c' direction.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792
-angles 90 125.4 90
1) Am i using the editconf in correct manner for generation of box for
the monoclinic crystal, though the crystal is of monoclinic i am

using box

Post by ramesh cheerla
type as triclinic
i haven't found any specific method for the generation of box for the
monoclinic crystal.
2) Is there any specific method to generate the box for the monoclinic
crystals.
3) The notations for the lattice parameters of the crystal i.e 'a' ,

'b'

Post by ramesh cheerla
, 'c' and angles alpha, beta , gamma used by crystallography and the

gromacs

Post by ramesh cheerla
editconf are the same or different, why because if i use editconf as

above i

Post by ramesh cheerla
WARNING: Triclinic box is too skewed.

your

Post by Mark Abraham
repeat post might be constructed so as to make it easier / more likely

for

Post by Mark Abraham
people help you. Likewise the final line of out_box.gro. Make sure you

have

Post by Mark Abraham
read and understood what documentation is available with editconf -h

and in

Post by Mark Abraham
manual section 3.2.
Mark
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Mark Abraham

2012-04-11 00:45:44 UTC

Isn't that a totally different box? See editconf -h about -angles.

Mark

Post by ramesh cheerla
in this case editconf haven't given any warning and the output as follows
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 1.477 0.167 0.675
1PEGA C2 2 1.487 0.085 0.804
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077
0.00000 -0.00000 -0.00000
Can you please help me in this regard.
thank you in advance.
On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham
Dear Gromacs users,
I am planing to simulate a polymeric
crystal in gromacs, which is of monoclinic unit cell with cell
parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta
= 125.4 deg. my crystal is of 424 type i.e 4 unit cells along
'a' direction '2' unit cells along 'b' direction and 4 unit
cells along 'c' direction.
So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.
editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608
7.792 -angles 90 125.4 90
1) Am i using the editconf in correct manner for generation of
box for the monoclinic crystal, though the crystal is of
monoclinic i am using box type as triclinic
i haven't found any specific method for the generation of box
for the monoclinic crystal.
2) Is there any specific method to generate the box for the
monoclinic crystals.
3) The notations for the lattice parameters of the crystal i.e
'a' , 'b' , 'c' and angles alpha, beta , gamma used by
crystallography and the gromacs editconf are the same or
different, why because if i use editconf as above i am getting
WARNING: Triclinic box is too skewed.
This means equation 3.3 of the manual is not true. Maybe beta
should be acute? I've no idea of necessity or convention here.
Inspecting the whole output of editconf is probably instructive,
but you've kept all that information to yourself instead of
re-thinking how your repeat post might be constructed so as to
make it easier / more likely for people help you. Likewise the
final line of out_box.gro. Make sure you have read and understood
what documentation is available with editconf -h and in manual
section 3.2.
Mark
--
gmx-users mailing list gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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
<mailto:gmx-users-request at gromacs.org>.
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ramesh cheerla

2012-04-11 04:02:13 UTC

Thank you mark.

Post by ramesh cheerla
Dear Mark,
Thank you for reply, sorry for not being very clear, Here my
doubt is can i use triclinic box for the simulations of the crystal whose
unit cell is monoclinic. As i said earlier i have tried editconf as
editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792
-angles 90 125.4 90
it gave the following warning
WARNING: Triclinic box is too skewed.
for clarity here i am sending a part of the output file generated by the
editconf
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 -0.025 0.408 -0.045
1PEGA C2 2 -0.015 0.326 0.084
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.60800 6.35148 0.00000 0.00000 0.00000 0.00000
-4.51376 -0.00000
if i change the angles while using the editconf i observed the following
changes
editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792
-angles 90 90 125.4
Isn't that a totally different box? See editconf -h about -angles.
Mark
in this case editconf haven't given any warning and the output as follows
God Rules Over Mankind, Animals, Cosmos and Such
6528
1PEGA C1 1 1.477 0.167 0.675
1PEGA C2 2 1.487 0.085 0.804
::::::::::::::::::::::::::::::::::::::::::::::::::::::::;
3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077 0.00000
-0.00000 -0.00000
Can you please help me in this regard.
thank you in advance.