Hi Gromacs users,
I am doing the protein lipid system packing step and thus shrinking and
minimizing the system alternately but after first minimization rest of all
minimization steps show E pot=nan and no minimization step occurs in the
em.log file. How to get rid of this problem? Please help.
On 14/09/2011 5:29 PM, madhumita das wrote:
Hi Gromacs users,
I am doing the protein lipid system packing step and thus shrinking
and minimizing the system alternately but after first minimization
rest of all minimization steps show E pot=nan and no minimization step
occurs in the em.log
Hello Users,
Previous I have done simulation of small protein using Amber10 with ff99sb
force field. I did the same calculation using the gromacs 4.5.1 with amber
ff99sb force field. I found a loop segment takes much more fluctuation with
gromacs simulation and which was not observed with
vijayaraj ramadoss wrote:
Hello Users,
Previous I have done simulation of small protein using Amber10 with
ff99sb force field. I did the same calculation using the gromacs 4.5.1
with amber ff99sb force field. I found a loop segment takes much more
fluctuation with gromacs simulation and
Please keep this discussion on the gmx-users list. I have only limited
experience with MARTINI, but there are others on the list more experienced than
I. See comments below.
Du Jiangfeng (BIOCH) wrote:
Dear Justin,
Thank you very much again of your help.
So far, I appended some
Hi,
On 9/13/11 4:27 PM, Mark Abraham wrote:
On 14/09/2011 12:20 AM, Marcin Zielinski wrote:
Ok,
Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors
during the compilation.
Firstly, including config.h inside the fortran .F kernel files for
power6 is causing problems with
their
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure out
when we are referring to equilibration which of the run time or n_steps
parameters are important. One could run 1,000,000 steps with dt of 0.001 ps
or
Juliette N. wrote:
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure out
when we are referring to equilibration which of the run time or n_steps
parameters are important. One could run 1,000,000
Hi,
I have not followed the entire discussion so I might be completely
wrong, I might be fill in some gaps.
Firstly, including config.h inside the fortran .F kernel files for power6 is
causing problems with
their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a
modified
On 15/09/2011 5:13 AM, Juliette N. wrote:
Hello,
For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure
out when we are referring to equilibration which of the run time or
n_steps parameters are important. One
Hi,
Please keep discussions on the mailing list. I have no experience of
Martini, and don't have the ability to give my time for individual help.
I would advise you to simplify your system as much as you can. Get a
stable simulation of a single glutamate residue working, then change to
a
Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr file. From
that I generated a .gro file using editconf. What it looks like now is it
starts numbering from 1 -29, which is where the first monomer ends, again 1-29
for the second monomer and then its continuous
On 15/09/2011 11:23 AM, Sweta Iyer wrote:
Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr
file. From that I generated a .gro file using editconf. What it looks
like now is it starts numbering from 1 -29, which is where the first
monomer ends, again 1-29 for
Mark Abraham wrote:
On 15/09/2011 11:23 AM, Sweta Iyer wrote:
Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr
file. From that I generated a .gro file using editconf. What it looks
like now is it starts numbering from 1 -29, which is where the first
You can either use -ighn option in pdb2gmx or mannualy rename the atom names in
the pdb file.
Cheers,
Jianguo
From: KONG Xian xiansh...@gmail.com
To: gmx-users@gromacs.org
Sent: Tuesday, 13 September 2011 15:36:41
Subject: [gmx-users] how to handle different
Hi Alan,
For example, in the Glycam_06g.dat file, you can find:
OH-CG-CG-OS 1 -1.10 0.0-1
So this dihedral parameter has a force constant of -1.10, and this is what I
mean by GLYCAM force field assigns negative force constants to some
dihedrals.
I did
Thanks Mark and Justin for your input. it works. For progeny, here's how:
1. In case of multiple, separate chains of protein, generate a *new* tpr X
that does not include chain information.
2. From X generate a new tpr file Y, consisting now only of the group under
scrutiny (for example,
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