- Original Message -
From: Manik Mayur manik.ma...@gmail.com
Date: Monday, August 16, 2010 3:02
Subject: Re: [gmx-users] Parallel mdrun not working on gentoo linux
To: Discussion list for GROMACS users gmx-users@gromacs.org
comments inline..
2010/8/14 Mark Abraham
Hello Sir,
I am simulating a protein which is a homodimer, when I did pdb2gmx, it
generated a topolgy file in which there were two chain topologies for each
chain as :
; Include chain topologies
#include topol_A.itp
#include topol_B.itp
and in Compound section gave ;
Hi,
I don't understand why 4.0.7 gives a segv.
But 4.5-beta probably gives a segv because of a parallel problem.
Could you try 4.5-beta with the mdrun option -nt 1
and report back?
Thanks,
Berk
Date: Fri, 13 Aug 2010 18:35:55 +0200
From: j...@um.es
To: gmx-users@gromacs.org
Subject:
Hi ALL,
I have made a CGMD system with multiple copies of a single protein in
bilayer, by replicating the monomer using genconf in the X-Y plane. After
running CGMD for about 100 ns, I am getting the following error:
onetwo wrote:
Hello Sir,
I am simulating a protein which is a homodimer, when I did pdb2gmx, it
generated a topolgy file in which there were two chain topologies for
each chain as :
; Include chain topologies
#include topol_A.itp
#include topol_B.itp
and in Compound section gave ;
Although a bit worrying the curvature of your bilayer is not
responsible for the error message you are seeing.
to solve the problem you have to increase to use the -rrd option
(see manual for explanation). Typicaly a value of 1.4 to 1.6 should
be fine.
On Aug 16, 2010, at 12:16 PM, Anirban
The way you define things would work fine but if
your dimer is an homodimer only one topology is
needed. topol_A and topolo_B should be identical.
The part of the mdp file is fine.
On Aug 16, 2010, at 7:13 AM, onetwo wrote:
Hello Sir,
I am simulating a protein which is a homodimer, when I
Thanks a lot XAvier for clarifying my doubt. You mean to say -rdd option
with mdrun, right? And why does this curvature of the membrane occurs?
Thanks a lot once again.
Regards,
Anirban
On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole x.peri...@rug.nl wrote:
Although a bit worrying the
So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.
Maiki wrote:
Hi,
I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff
$ pdb2gmx -f del.pdb -o
On 2010-08-16 12.34, Maiki wrote:
So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.
Not all force fields have complete support for DNA. Try Charmm.
Maiki wrote:
Hi,
Hi Javier,
I've just committed a fix to the git 4.5 tree. Thanks for reporting this.
Sander
On 13 Aug 2010, at 18:35 , Javier Cerezo wrote:
Hi all.
I am trying to perform a tpi (test particle insertion) calculation on a
trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a
Anirban Ghosh wrote:
Hi ALL,
I have made a CGMD system with multiple copies of a single protein in
bilayer, by replicating the monomer using genconf in the X-Y plane.
After running CGMD for about 100 ns, I am getting the following error:
/20100816/b7ad9340/attachment-0001.html
--
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
-
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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gmx-users mailing listgmx-users@gromacs.org
http
David van der Spoel wrote:
On 2010-08-16 12.34, Maiki wrote:
So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.
Not all force fields have complete support for DNA. Try
On 2010-08-16 14.44, Maiki wrote:
David van der Spoel wrote:
On 2010-08-16 12.34, Maiki wrote:
So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.
Not all force fields
- Original Message -
From: onetwo twoon...@rediffmail.com
Date: Monday, August 16, 2010 18:55
Subject: [gmx-users] Running MD on a dimeric protein
To: gmx-users@gromacs.org
Hello Sir,
I am simulating a protein which is a homodimer, when I did pdb2gmx, it
generated a topolgy
Hello Sir,
I am simulating a protein which is a homodimer, when I did pdb2gmx, it
generated a topolgy file in which there were two chain topologies for each
chain as :
; Include chain topologies
#include topol_A.itp
#include topol_B.itp
and in Compound section gave ;
On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote:
Thanks a lot XAvier for clarifying my doubt. You mean to say -rdd
option with mdrun, right?
yes
And why does this curvature of the membrane occurs?
No idea!
Thanks a lot once again.
Regards,
Anirban
On Mon, Aug 16, 2010 at 3:53 PM,
Hello,,
I am really thankful to Mark, Justin and XAvier for helping me to clear my
doubts.
Reply by Mark is really explainatory. I got my doubts clear.
Regards
Note: Forwarded message attached
-- Original Message --
From: onetwo twoon...@rediffmail.com
To: gmx-users@gromacs.org
Subject:
Hi,
I am looking for OPLS parameters for heme. Does anyone has the parameters and
would be able to provide it?
Any help or suggestions would be appreciated.
Thanks
Shabana
---
Shabana Vohra
SBCB Unit,Department of
David van der Spoel wrote:
On 2010-08-16 14.44, Maiki wrote:
David van der Spoel wrote:
On 2010-08-16 12.34, Maiki wrote:
So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without
Hello,
I want to simulate a simple NaCl ion in water. I know the method
using genion which adds individual Na+ and Cl- ion, but I wish to
simulate Na-Cl connected rather than free ions floating in water. When
I ran the grompp command I got the error:
No default Bond types
So I am
HI
What is the math definition of the radii of gyration about the principal
axes in Gromacs?
I use the command g_gyrate -p
For lysozyme , I got =
0.922754 1.22249 1.25603
but in some paper, the authors got
= 0.660 0.833 0.991
It is a quite difference.
From David =
The
On 2010-08-16 20.15, Chih-Ying Lin wrote:
HI
What is the math definition of the radii of gyration about the principal
axes in Gromacs?
I use the command g_gyrate -p
For lysozyme , I got =
0.922754 1.22249 1.25603
but in some paper, the authors got
= 0.660 0.833
nishap.pa...@utoronto.ca wrote:
Hello,
I want to simulate a simple NaCl ion in water. I know the method
using genion which adds individual Na+ and Cl- ion, but I wish to
simulate Na-Cl connected rather than free ions floating in water. When I
ran the grompp command I got the error:
No
- Original Message -
From: nishap.pa...@utoronto.ca
Date: Tuesday, August 17, 2010 3:56
Subject: [gmx-users] NaCl
To: gmx-users@gromacs.org
Hello,
I want to simulate a simple NaCl ion in
Well, technically not an ion. I reckon that even given Moore's Law will
continue to hold,
I believe the bonds are not defined in the OPLS-AA force field for
NaCl. I know this might sound like a stupid question, but is there a
way to determine the bond force constant (kb), I tried to look it up,
but I couldn't find anything.
Quoting Justin A. Lemkul jalem...@vt.edu:
nishap.pa...@utoronto.ca wrote:
I believe the bonds are not defined in the OPLS-AA force field for NaCl.
I know this might sound like a stupid question, but is there a way to
determine the bond force constant (kb), I tried to look it up, but I
couldn't find anything.
There may be
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