Dear list,
I am trying to extract energy profile for a protein molecule using rerun
program from trajectory obtained by MD of protein solvated in a water box. I
have created index file and reedited the original mdp file (removed the SOLs
from it) to get a new tpr file using grompp. I have
Hi,
The cosine content is not the most important property you should look at.
Like any type of analysis, you should check the convergence.
The simplest way of doing this is cutting your trajectory in, for instance,
four parts and determining the correlation.
g_anaeig will always print the
On Jan 10, 2009, at 8:32 PM, Nicolas wrote:
Berk Hess a écrit :
Hi,
Setting -npme 2 is ridicolous.
mdrun estimates the number of PME nodes by itself when you do not
specify -npme.
In most cases you need 1/3 or 1/4 of the nodes doing pme.
The default -npme guess of mdrun is usually not bad,
From: ckut...@gwdg.de
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Best performace with 0 core for PME calcuation
Date: Mon, 12 Jan 2009 10:41:26 +0100
On Jan 10, 2009, at 8:32 PM, Nicolas wrote:
Berk Hess a écrit :
Hi,
Setting -npme 2 is ridicolous.
mdrun estimates the
Hello,
I am trying to do REMD for a protein unfolding. I am following the information
given in http://wiki.gromacs.org/index.php/REMD but I am completely new in
these type of simulations. I would like to ask two questions to more advanced
users. I hope you could help me:
-I have seen that
Rebeca García Fandiño wrote:
Hello,
I am trying to do REMD for a protein unfolding. I am following the
information given in http://wiki.gromacs.org/index.php/REMD but I am
completely new in these type of simulations. I would like to ask
two questions to more advanced users. I hope you could
Dear all,
I wonder if you could let me know of any program or script available in
order to calculate Scd order parameter in a vesicle.
Best regards
Cesar Avila
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Dear users,
I would like to carry out steered molecular dyanmics simulations on one of
my protein dimer. I have a few questions to learn regarding this.
1. The mdrun program needs -pn index.ndx file
The way I understand is, we need to create the index file with groups (say
atom1 to which the
My mistake. I suggest 500 kJ/mol/nm^2, not 500 kcal... sorry.
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Carsten Kutzner a écrit :
On Jan 10, 2009, at 8:32 PM, Nicolas wrote:
Berk Hess a écrit :
Hi,
Setting -npme 2 is ridicolous.
mdrun estimates the number of PME nodes by itself when you do not
specify -npme.
In most cases you need 1/3 or 1/4 of the nodes doing pme.
The default -npme guess of
Nicolas wrote:
Carsten Kutzner a écrit :
On Jan 10, 2009, at 8:32 PM, Nicolas wrote:
Berk Hess a écrit :
Hi,
Setting -npme 2 is ridicolous.
mdrun estimates the number of PME nodes by itself when you do not
specify -npme.
In most cases you need 1/3 or 1/4 of the nodes doing pme.
The
Hello,
I have a problem in the generation of the topology file of a ligand
using x2top program..I am
using the version 3.3.3 of Gromacs.
Here is the command that i used and the error am getting,
x2top -f chop.pdb -o dpppc.top
Can not find forcefield for atom OW-16850 with 2 bonds
Can not find
krithika krishnaswamy wrote:
Hello,
I have a problem in the generation of the topology file of a ligand
using x2top program..I am
using the version 3.3.3 of Gromacs.
Here is the command that i used and the error am getting,
x2top -f chop.pdb -o dpppc.top
This program has limited use for small
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