Good place to have a read is:
http://wiki.gromacs.org/index.php/Category:Force_Fields
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
pragya chohan wrote:
hi... i have to make an itp file for alamethicin already tried
prodrg2 but no success. pls suggest a way for making .itp file
.. residue already defined in ffgmx.rtp. ...already read
earlier query posted but could not find an ans.
pls rite norml Engspea
pragya chohan wrote:
hi... i have to make an itp file for alamethicin already tried prodrg2 but
no success. pls suggest a way for making .itp file .. residue already
defined in ffgmx.rtp. ...already read earlier query posted but could not find
an ans.
pls rite norml Engspeak in
[EMAIL PROTECTED] wrote:
Sir:
How are you! I am a new user of gmx.At first,sincere tribute to you and all
the gmx developers!
I want to perform a molecular dynamics simulation on the tobramycin aqueous
soluton by gmx. On the simulation process,I encounter some problem and I can't
treat w
hi... i have to make an itp file for alamethicin already tried prodrg2 but
no success. pls suggest a way for making .itp file .. residue already
defined in ffgmx.rtp. ...already read earlier query posted but could not find
an ans.
___
Hi, Dr. Liang
Please use PRODRG server.
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
or you can write some script to convert Material studio pdb file to PDB bank
format.
Thanks.
On 10/31/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
> Sir:
> How are you! I am a new user of gmx.At f
Sir:
How are you! I am a new user of gmx.At first,sincere tribute to you and all
the gmx developers!
I want to perform a molecular dynamics simulation on the tobramycin aqueous
soluton by gmx. On the simulation process,I encounter some problem and I can't
treat with it by myself and I hope
[EMAIL PROTECTED] wrote:
Hi, all
I have simulated a beta-hairpin folded in explicit water, I want to
compare
the simulated structure to the experimental structure using NMR. Can you tell me
how to do it? Thanks a lot!
fufengliu
Look in GROMACS manual section 7.4 for clues
Hi, all
I have simulated a beta-hairpin folded in explicit water, I want to
compare
the simulated structure to the experimental structure using NMR. Can you tell me
how to do it? Thanks a lot!
fufengliu
___
gmx-users mailing list
marcos wrote:
Hi,
editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
should be "%8.3f%8.3f%8.3f".
Also the charges and radius are written in "%8.4f%8.4f" while the
program pdb2pqr writes as "%8.4f%7.4f"
I changed line 167 of pdbio.c from:
strcpy(pdbform,"%-6s%5u %-4.4s %3.
Ricardo Gobato wrote:
In middle on molecular danimics have one bug power energy, have one exit
the file traj.trr
For continuity md with file traj.trr, write the comand
1. Don't claim a bug unless you actually have one - i.e. have at least a
reproducible test case, and preferably code patch to
In middle on molecular danimics have one bug power energy, have one exit the
file traj.trr
For continuity md with file traj.trr, write the comand
..
_
Conheça o Windows Live Spac
Dear Marcin,
You can contact me off list for a script that calculates the QH entropies
from the output of g_covar. Also, IIRC there should be a version of g_covar
that already does it somewhere (CVS-?).
Ran.
On Wed, 31 Oct 2007 17:40:45 +
Marcin Krol <[EMAIL PROTECTED]> wrote:
Dear All
3.3.1 and 3.3.2
IIRC in 3.1.4 it was ok
Marcos
On Wed, 2007-10-31 at 18:34 +0100, Ran Friedman wrote:
> Dear Marco,
>
> Which version?
>
> Ran.
>
> marcos wrote:
> > Hi,
> >
> > editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
> > should be "%8.3f%8.3f%8.3f".
> > Also
Dear All,
Sorry for the repeated question, but I'm a bit lost when I want to get
frequencies of modes from quasiharmonic analysis done with g_covar. From
what I understood in QH
omega = sqrt(kT/lambda), where omega is the radial frequency, k -
Boltzmann const, T-temp, and lambda is the eigenva
Dear Marco,
Which version?
Ran.
marcos wrote:
> Hi,
>
> editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
> should be "%8.3f%8.3f%8.3f".
> Also the charges and radius are written in "%8.4f%8.4f" while the
> program pdb2pqr writes as "%8.4f%7.4f"
>
> I changed line 167 of p
Hi,
editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
should be "%8.3f%8.3f%8.3f".
Also the charges and radius are written in "%8.4f%8.4f" while the
program pdb2pqr writes as "%8.4f%7.4f"
I changed line 167 of pdbio.c from:
strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%10
I have aprox. 81000 atoms. The system worked on a Itanium 2 cluster.
On the IBM machine I've used the IBM compilers.
I'm going to give it a try with gcc.
Thank you
Marius Retegan
On 10/31/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Marius Retegan wrote:
> > 32 Gb on each node of the clust
Tommy Carstensen wrote:
To the gmx-users,
When executing:
g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso
I get the following error after running through all the frames:
Segmentations fault
If I don't include the aniso flag I don't get an segfault. Can anyone
explain to me, why it is not wo
To the gmx-users,
When executing:
g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso
I get the following error after running through all the frames:
Segmentations fault
If I don't include the aniso flag I don't get an segfault. Can anyone
explain to me, why it is not working with the aniso flag?
tangxuan wrote:
Hi Mark,
Thanks very much for your reply. I checked the structure of A and B at
these three ps, and there is no much change in the structures. Then I
calculated the reside area in A+B at these three specific time
(1536,15937,15938), and it shows that there are a big diffrence in
Hi Mark,
Thanks very much for your reply. I checked the structure of A and B at
these three ps, and there is no much change in the structures. Then I
calculated the reside area in A+B at these three specific time
(1536,15937,15938), and it shows that there are a big diffrence in size
of area at ma
Marius Retegan wrote:
32 Gb on each node of the cluster.
Maybe I should add that I've also ran CPMD and cp2k jobs on the
cluster but I've never had memory problems.
Marius Retegan
It could still be too little, since this is the additional memory. What
kind of system are you using, how many atoms
pragya chohan wrote:
hi ... when i run grompp i get an error " No such moleculetype Protein " ... i
included itp for ACE and AIB after generating them from PRODRG2 server... my top file is :
Check out
http://wiki.gromacs.org/index.php/Errors#Fatal_error:_No_such_moleculetype_XXX
Mark
__
hi ... when i run grompp i get an error " No such moleculetype Protein " ... i
included itp for ACE and AIB after generating them from PRODRG2 server... my
top file is :
; Include forcefield parameters
#include "ffG43a1.itp"
; Include chain topologies
#include "ace.itp"
#include "aib.itp"
; I
32 Gb on each node of the cluster.
Maybe I should add that I've also ran CPMD and cp2k jobs on the
cluster but I've never had memory problems.
Marius Retegan
On 10/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Marius Retegan wrote:
> > Dear Gromacs users
> >
> > I'm having some troubles
himanshu khandelia wrote:
> Hi Carsten,
>
> The benchmarks were made is 1 NIC/node, and yet the scaling is bad.
> Does that mean that there is indeed network congestion ? We will try
> using back to back connections soon,
Hi Himanshu,
In my opinion the most probable scenario is that the bandwidt
From: "Syma Khalid" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
To: "'Discussion list for GROMACS users'"
Subject: [gmx-users] langevin dynamics
Date: Tue, 30 Oct 2007 16:55:59 -
Dear all,
I was wondering if someone could offer some advice?
I
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