Dear Users,
when trying to run the following command:
mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
I have received the error below.
Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads
---
P
On Fri, Jun 7, 2013 at 11:52 AM, Mark Abraham wrote:
> If you want to suggest fixing any possible problem, please file an issue at
> redmine.gromacs.org
>
There is already a report in redmine with a suggestion on how to deal
with NaNs: http://redmine.gromacs.org/issues/941
On Thu, Jun 6, 2013 a
On 7/20/13 9:12 AM, rama david wrote:
Dear Justin,
Thank you for your Prompt Reply.
I run a at least 4-5 run of each peptide.
The result are like the xx peptide form beta structure early than yy
peptide in each run.
I just used the different tau_P ( relaxation time ) for NPT and MD
product
On 7/20/13 7:35 AM, afsaneh maleki wrote:
Dear users
To generate a topology file for an arbitrary molecule, I used g_x2top
program.
I added following lines to atomname2type.n2t:
..
..
C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149
C opls_145B 0.091698 12.0110 3
Problem partly addressed. If I run normal modes in -nt 1, then I get
the same force as after the minimization.
I'll file a redmine.
On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts wrote:
> To follow up -- if I try to minimize again using -t, I get the same
> low forces as in the minimization in
To follow up -- if I try to minimize again using -t, I get the same
low forces as in the minimization in the previous step. So it appears
to be something with what do_nm is doing, not with errors in the
output structure.
On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts wrote:
> When I minimize a
When I minimize a structure, I can get down to the force max being <0.01
Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
Potential Energy = -5.12340607768673e+03
Maximum force = 6.68907856457542e-03 on atom 3029
Norm of force = 2.19978176343026e-03
kJ/nm. However, whe
Dear Justin,
Thank you for your Prompt Reply.
I run a at least 4-5 run of each peptide.
The result are like the xx peptide form beta structure early than yy
peptide in each run.
I just used the different tau_P ( relaxation time ) for NPT and MD
production run.
XX tau_p = 2 YY
Hello,
Following the Section 5.3.2 of the manual, I have tried to set the C6
term of the non-bonded (Lennard-Jones) interaction to zero as follows:
"When sigma and epsilon need to be supplied (rules 2 and 3), it
would seem it is impossible to have a non-zero C12 combined with a
zero C6 paramete
Hello,
I am not sure whether this is a known problem, but it seems
gromacs-4.5.7 compilation using autoconf tool is still broken (at
least for me). The ./configure step completes without any error. But
"make" fails with the following error regarding not finding certain
version of aclocal and autom
Dear Justin,
Thank you very much from your response.
Best Regards
Sara
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Saturday, July 20, 2013 3:47 PM
Subject: Re: [gmx-users] old and new versions of gromacs
On 7/20/13
Dear users
To generate a topology file for an arbitrary molecule, I used g_x2top
program.
I added following lines to atomname2type.n2t:
..
..
C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149
C opls_145B 0.091698 12.0110 3 C 0.149 C 0.1395 C 0.1395
..
But, generate
On 7/20/13 5:27 AM, rama david wrote:
Dear Friends,
I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )
In First Experiment, I put the two XX peptide far from each other 2.0 nm,
and run the simulation.
In the second experiment I put the two
On 7/20/13 2:58 AM, mohammad agha wrote:
Dear Gromacs Specialists
I already worked with Gromacs-4.5.4. In the Gromacs site has been released new
several versions. Has the old version (4.5.4) defects? Or are the new versions
more complete? I want to continiue my simulations with 4.5.4, are th
Dear Friends,
I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )
In First Experiment, I put the two XX peptide far from each other 2.0 nm,
and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the
Soneone said here that static versions are impossible for Cray...
Dr. Vitaly V. Chaban
On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner wrote:
> Hi
>
> I am having problems creating static versions of the GROMACS binaries for
> a Cray XE6 (www.hector.ac.uk). The build process I am using is d
Dear Gromacs Specialists
I already worked with Gromacs-4.5.4. In the Gromacs site has been released new
several versions. Has the old version (4.5.4) defects? Or are the new versions
more complete? I want to continiue my simulations with 4.5.4, are there
problems for it?
I compared the manual o
Dear Gromacs Specialists
I already worked with Gromacs-4.5.4. In the Gromacs site has been released new
several versions. Has the old version (4.5.4) defects? Or are the new versions
more complete? I want to continiue my simulations with 4.5.4, are there
problems for it?
I compared the manual o
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