Sorry
I will take care of this in the future.
Thanks for your advice .
On 6/29/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> i m carryin a protein explicit solvent simulation using gromacs 3.3
> for intially minimizing the hydrogen i did some small mini and equi in
the
> vaccum by maintaing
> i m carryin a protein explicit solvent simulation using gromacs 3.3
> for intially minimizing the hydrogen i did some small mini and equi in the
> vaccum by maintaing the restraints
> then i added ions and water but in the very first minimization i m getting
> the following error
Please use no
> Hi,
> I am new to GROMACS. I want to perform Normal Mode Analysis of a protein.
> For that I require a well minimized structure. I have minimized my
> structure
> using steepest descent and conjugate gradient. But the structure seems to
> have got struct in a local energy minima. How should I pro
i m carryin a protein explicit solvent simulation using gromacs 3.3
for intially minimizing the hydrogen i did some small mini and equi in the
vaccum by maintaing the restraints
then i added ions and water but in the very first minimization i m getting
the following error
1-4 interaction betwe
Hi,
I am new to GROMACS. I want to perform Normal Mode Analysis of a protein.
For that I require a well minimized structure. I have minimized my structure
using steepest descent and conjugate gradient. But the structure seems to
have got struct in a local energy minima. How should I proceed to get
Great thanks, I had no idea such a tool existed.
Also, if we're doing Xenon in water (spc) simulations, we have to
parameterize the nonbonded interactions between OW and Xe, and H and Xe,
right? That parameterization doesn't already exist, or does it?
David van der Spoel wrote:
Arneh Babakh
[EMAIL PROTECTED] wrote:
hello all,
I am trying to get the best representative structure of a 40ns MD of a
receptor to use for free energy calculations.
I want to have an idea what is the best way to do that.
I am using g_cluster with the gromos method. Is there a way to estimate
the noise e
Dave Segala wrote:
Hi all,
I am using the opls-aa force field to simulate my molecule. I have files
which ran correctly on version 3.2.1 and are not running on version 3.3.
When I use the command pdb2gmx I encounter many errors:
1. wrong input on ffolpsaa.hdb file
2 7 OW
when I change to 2
hello all,
I am trying to get the best representative structure of a 40ns MD of a
receptor to use for free energy calculations.
I want to have an idea what is the best way to do that.
I am using g_cluster with the gromos method. Is there a way to estimate
the noise errors of the cluster analysi
Hi all,
I am using the opls-aa force field to simulate my molecule. I have files
which ran correctly on version 3.2.1 and are not running on version 3.3.
When I use the command pdb2gmx I encounter many errors:
1. wrong input on ffolpsaa.hdb file
2 7 OW
when I change to 2 7 HW OW, it works.
2
From: Jiang ran <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To:
Subject: [gmx-users] BUG: FENE bond stretching potential
Date: Thu, 28 Jun 2007 23:07:55 +0800
Hello people,My professor and I tried to use the FENE potentials to relax a
protein from a unstable config
Hello people,My professor and I tried to use the FENE potentials to relax a
protein from a unstable configuration for publishing paper. However, these
potentials didn't seem to work. Checking both the manual and the code of the
GROMACS software package for moleculair dynamics we found some thi
> Hi Gurpreet,
>
> 1. http://wiki.gromacs.org/index.php/GROMOS (note term "united atom")
> 2. http://wiki.gromacs.org/index.php/Manual:grompp_3.3.2 (check -r)
>
> In addition, read Chapter 5 of the manual, regarding topologies (and
> the file format, #include statements and "position_restraints")
>
Hi Gurpreet,
1. http://wiki.gromacs.org/index.php/GROMOS (note term "united atom")
2. http://wiki.gromacs.org/index.php/Manual:grompp_3.3.2 (check -r)
In addition, read Chapter 5 of the manual, regarding topologies (and
the file format, #include statements and "position_restraints")
Wow.., that
hello gromacs users
my question is regarding the command pdb2gmx which is the first step to
process ur input file. i used the force field 43a1 and i m doing some
dimeric protein simulation . when i checked the output of the pdb2gmx
command i found that this command have not added any hydrogens to
Martin Höfling a écrit :
Am Mittwoch, 27. Juni 2007 schrieb David van der Spoel:
So the submitted script was basically calling a python script, calling
the necessary tools to check output, and run the next step. This can be
cumbersome, if it comes to errorhandling (hardware failures etc.)
actu
Hi Abu,
with these commands you download the latest CVS version:
cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login
cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx
Carsten
Naser, Md Abu wrote:
> > I implemented an xy only fitting option for trjconv in the development
>
> Ok, I solved the problem. To access the programs in directory directly,
> you have put this path into your PATH
> declaration. One way to do this permanently is to add it to your .bashrc
> file. and add the line
>
> export PATH=/home/mydirectory/gromacs-3.3/src/kernel/:$PATH
>
> Then save the f
Arneh Babakhani wrote:
Hi GMX community,
We're doing some MD involving Xenon atoms. For our parameterization, we
obtained sigma and epsilon (over kB) values of 3.975 Ang. and 214.7 K,
from the following JCP reference:
http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPS
Ok, I solved the problem. To access the programs in directory directly, you
have put this path into your PATH
declaration. One way to do this permanently is to add it to your .bashrc file.
and add the line
export PATH=/home/mydirectory/gromacs-3.3/src/kernel/:$PATH
Then save the file, and typ
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