On 6/26/13 4:12 PM, HANNIBAL LECTER wrote:
It is not very clear as to what you are trying to do? If you have the final
coordinates and velocities from a previous simulation, I would recommend
start a simulation using the .gro file and ensuring that you have
gen-vel=no in the .mdp file.
If you
It is not very clear as to what you are trying to do? If you have the final
coordinates and velocities from a previous simulation, I would recommend
start a simulation using the .gro file and ensuring that you have
gen-vel=no in the .mdp file.
If you have a well-equilibrated system, then the prope
On 11/12/2010 2:19 AM, Anna Marabotti wrote:
Dear all,
I conserved all the files produced sometimes ago with a simulation
made with Gromacs 3.3.3 installed on a cluster. I would like to
prolonge this simulation, but I have no longer access to that cluster,
instead I can access another cluster
Milan Melichercik wrote:
On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote:
Hi everyone,
It's the first I use the process of extending simulations.
I did the following:
tpbconv -s prot.tpr -extend 6000 -o protein.tpr
mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr
On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote:
> Hi everyone,
>
> It's the first I use the process of extending simulations.
> I did the following:
> tpbconv -s prot.tpr -extend 6000 -o protein.tpr
>
> mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c
> protein.gr
Hello,
I am having a similar issue. When using Gromacs version 4.0.4 and
running mdrun with the -append flag on a traj.trr file over 2GB I get
an error stating "Truncation of traj.trr file failed". However, when I
use version 4.0.2 it seems to append fine even with very large files.
Any ideas as t
file i am waiting for
your reply
thanks in Advance
--- On *Wed, 6/5/09, kyungchan chae //* wrote:
From: kyungchan chae
Subject: RE: [gmx-users] extending simulations
To: "'Discussion list for GROMACS users'"
Date: Wednesday, 6 May,
: No such file or directory
please kindly rectify the error in the configure file i am waiting for your
reply
thanks in Advance
--- On Wed, 6/5/09, kyungchan chae wrote:
From: kyungchan chae
Subject: RE: [gmx-users] extending simulations
To: "'Discussion list f
If you want to extend your simulation, simply use the 'append' command.
: mdrun -append yes -cpi state.cpt
Extending a simulation is quite simple. However, if your trajectory file is
larger than 2GB, you are going to have a problem. I tested it a few weeks
ago and found out that the 'append' opti
Anna Marabotti wrote:
Dear all,
I'd need to have a clarification about how to extend a simulation made using
GROMACS 4 that has been
interrupted on a system due to walltime expiration. On the Wiki section I see:
"A simulation that has completed is extended using tpbconv, mdrun and
checkpoint
You can use the mdrun command:
How to restart a crashed run. The mdrun program now uses a very handy
checkpointing feature.
Restarting crashed runs is easy with mdrun.
mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr –g prev.log –cpi -append
在2009-05-06，"Anna Marabotti" 写道：
>Dear al
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