I have used demux.pl from gromacs 4.6.3 on files up to 1 us per replica
simulated with gromacs 4.6.1. For my usage, the first column of both output
.xvg files (replica_index.xvg and replica_temp.xvg) is fine up to 1
microsecond, then moves to scientific notation but, unfortunately, there are
Say you have a box with an x-side length of 3 nm and two atoms with x-dimension
position restraints to: (a) x=1 nm, and (b) x=2 nm
Then let the box shrink to 99% of its previous size due to pressure coupling.
The following is my understanding of the locations to which the atoms will be
where do you learn this stuff ? ;)
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul
jalem...@vt.edu
Sent: 22 March 2014 21:50
To: gmx-us...@gromacs.org
Subject: Re:
My colleague and I have simulated atomistic polymers containing PEG. If the
issue is just parameters, you can find them here:
http://pubs.rsc.org/en/content/articlelanding/2010/sm/c001988g#!divAbstract
From:
I have run into similar error messages running gromacs 4.6.2 on some new
Xeon's. That cluster is having file system problems sporadically and I end up
with jobs that die about 1% of the time with message like this:
mdrun_mpi:21408 terminated with signal 6 at PC=38e02328a5 SP=7f534f467738.
I've run gromacs v4.6.3 on BG/Q without problem and my colleagues have run
older versions of gromacs on the BG/L also without problem. (No BG/P
experience here, unfortunately). Still, it's worth having you post your job
submission script for us to take a look at.
Also, is it just gromacs
It could be a quota issue (there is free space, but your group has used its
entire allocation). Also, file systems often have limits not only on the total
amount of space, but also on the total number of files that a group is allowed
to create. Talk to your system administrator. There is likely
It's not US if you have a non-zero pull-rate1 that gets applied during your
simulation, although with your pull-geometry=distance I don't think that
pull-rate is even used (therefore I think that part is technically correct,
although your .mdp file is confusing on this issue).
Careful that X
Presuming that you have indeed set up the number of processors correctly
(should be running on a different number of cored for different number of
replicas to do a fair test), could it be a thread pinning issue?
I run on a Nehalem system with 8 cores/node but, because of the Nehalem
down drastically
On Feb 24, 2014 11:01 PM, Christopher Neale chris.ne...@alum.utoronto.ca
wrote:
Presuming that you have indeed set up the number of processors correctly
(should be running on a different number of cored for different number of
replicas to do a fair test), could it be a thread
some literture about the effect of using the
NVT ensemble or the NPT one?
Is there any major difference between pull_geometry = direction-periodic
and pull_geometry = direction?
Thank you
Lalita
Message: 1
Date: Thu, 9 Jan 2014 16:32:27 +
From: Christopher Neale chris.ne...@alum.utoronto.ca
Try using
pull_geometry = direction-periodic
For more details, see http://bugzilla.gromacs.org/issues/1352
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Lalita Shaki
To help you, I need to see the exact commands that you used. Best is if you can
put it all in a script, run the script to be sure that you see the problem, and
then copy and paste the script back to this list. Failing that, copy and paste
your commands and tell me what your command-line input
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