[gmx-users] difficulties in creating octahedral boxes

[Astrid Maaß]

Dear all,

I am new to gromacs and exercising, thus currently I am trying to follow
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many
thanks) for my example molecule (alanine). I have used the sequence of
commands below:

pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top

When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the final
line in ex_in_box.gro seems to describe a non cubic box:
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
-0.81310 1.14989
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?

I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!

Kind regards,

Astrid Maa?

[David van der Spoel]

Post by Astrid Maaß
Dear all,
I am new to gromacs and exercising, thus currently I am trying to follow
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many
thanks) for my example molecule (alanine). I have used the sequence of
pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top
When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the final
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
-0.81310 1.14989
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?
I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!
Kind regards,
Astrid Maa?
_______________________________________________
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please read the manual, in particular chapter three, which explains
periodic boundary conditions and the different boxes.

[Ran Friedman]

Dear Astrid,

It seems as if the problem is in the presentation, not in GMX. trjconv
-ur compact may help.

Ran.

Post by Astrid Maaß
Dear all,
I am new to gromacs and exercising, thus currently I am trying to
follow the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan
(many thanks) for my example molecule (alanine). I have used the
pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top
When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
-0.81310 1.14989
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?
I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!
Kind regards,
Astrid Maa?
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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

--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. [phone]
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
------------------------------------------------------

[Hanna, Joanne]

Hi

If you do:
editconf -f box.gro -o box.pdb
and view this in rasmol entering the command
set unitcell on
you should see the octahedral box.
To view the octahedral box with the water you need to use the '-ur compact' option in trjconv.
This should give you the octahedral representation.

Jo



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Astrid Maa?
Sent: Mon 11/12/2006 10:53
To: gmx-users at gromacs.org
Subject: [gmx-users] difficulties in creating octahedral boxes

Dear all,

I am new to gromacs and exercising, thus currently I am trying to follow
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many
thanks) for my example molecule (alanine). I have used the sequence of
commands below:

pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top

When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the final
line in ex_in_box.gro seems to describe a non cubic box:
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
-0.81310 1.14989
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?

I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!

Kind regards,

Astrid Maa?


_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
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[Tsjerk Wassenaar]

Hi Astrid,

Besides all the useful advice regarding the visualization, note that
the rhombic dodecahedron is smaller than the truncated octahedron and
is more spherical, thus yields a more even distribution of water
around your solvent, rendering an effect due to the box type less
probable. In short, it's better to use a rhombic dodecahedron than a
truncated octahedron.

Cheers,

Tsjerk

Post by Hanna, Joanne
Hi
editconf -f box.gro -o box.pdb
and view this in rasmol entering the command
set unitcell on
you should see the octahedral box.
To view the octahedral box with the water you need to use the '-ur compact'
option in trjconv.
This should give you the octahedral representation.
Jo
-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Astrid Maa?
Sent: Mon 11/12/2006 10:53
To: gmx-users at gromacs.org
Subject: [gmx-users] difficulties in creating octahedral boxes
Dear all,
I am new to gromacs and exercising, thus currently I am trying to follow
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many
thanks) for my example molecule (alanine). I have used the sequence of
pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top
When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the final
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
-0.81310 1.14989
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?
I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!
Kind regards,
Astrid Maa?
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 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
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

[Samuel C Flores]

Hi Guys,



I have a question. I am using genion to add two ZN2+ ions to a protein that
already has two. I thought I would just use genion with ?np 2. However it
seemed to recognize that there were already two in the file and added none.
So instead I used the parameter ?np 4. This seemed to add two, for a total
of four, which I wanted. However sometimes it seems to add two too many!
Am I understanding the proper use of the ?np parameter?



Many thanks in advance.



Sam



Samuel Flores

Gerstein Lab

office:

266 Whitney Ave., Bass 437

New Haven, CT 06520

203.432.5405



Home:

120 Huntington Street

New Haven, CT 06511

cell: 203.747.2682

_____

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Hanna, Joanne
Sent: Monday, December 11, 2006 11:02 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] difficulties in creating octahedral boxes



Hi

If you do:
editconf -f box.gro -o box.pdb
and view this in rasmol entering the command
set unitcell on
you should see the octahedral box.
To view the octahedral box with the water you need to use the '-ur compact'
option in trjconv.
This should give you the octahedral representation.

Jo



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Astrid Maa?
Sent: Mon 11/12/2006 10:53
To: gmx-users at gromacs.org
Subject: [gmx-users] difficulties in creating octahedral boxes

Dear all,

I am new to gromacs and exercising, thus currently I am trying to follow
the "Gromacs tutorial for Drug-Enzyme complex" of J. Kerrigan (many
thanks) for my example molecule (alanine). I have used the sequence of
commands below:

pdb2gmx -f example.pdb -p ex.top -o ex_in.gro
editconf -f ex_in.gro -d 1.0 -bt octahedron -c -o ex_in_box.gro
genbox -cp ex_in_box.gro -cs -o ex_sol.gro -p ex.top
genbox -cp ex_in_box.gro -cs -o ex_sol.pdb -p ex.top

When viewing my system ex_sol.pdb with rasmol I notice that my alanine
molecule is placed near to one face (inspite of -c) of a rectangular
(inspite of -bt octahedron) box. editconf gives no warning and the final
line in ex_in_box.gro seems to describe a non cubic box:
2.43930 2.29979 1.99168 0.00000 0.00000 0.81310 0.00000
-0.81310 1.14989
When filling the box with water molecules by use of genbox again no
significant warning is given and the final line remains unaltered in
ex_sol.gro. So why do I see my alanine in a cube of water molecules?

I would appreciate any explanation or instruction how to create a
non-cubic system very much.
Thank you in advance!

Kind regards,

Astrid Maa?


_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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]

Post by Samuel C Flores
Hi Guys,
I have a question. I am using genion to add two ZN2+ ions to a protein that
already has two. I thought I would just use genion with ?np 2. However it
seemed to recognize that there were already two in the file and added none.
So instead I used the parameter ?np 4. This seemed to add two, for a total
of four, which I wanted. However sometimes it seems to add two too many!
Am I understanding the proper use of the ?np parameter?

If it "seemed" to add two too many, then the most likely cause was that
you had fewer ions in your input structure than you thought you had. You
should check out the man page for genion, and consider using -pq.

Mark