[gmx-users] tpbconv restart crashing on 3.3.1

Alan Dodd anoddlad at yahoo.com
Mon Jun 11 15:24:19 CEST 2007

yes, tpbconv has been given the energy file.  gmxcheck says trr and edr files look happy, the original .tpr looks fine from gmxdump and doesn't crash when it's rerun, and any output from tpbconv looks fine from scanning bits of it in text format, though it's a pretty massive file and I've no idea what I'm looking for.  Any suggestions as to keywords to run searches for in these files?  I've tried various permutations of warning, error, etc. 

----- Original Message ----
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, June 10, 2007 4:15:29 PM
Subject: Re: [gmx-users] tpbconv restart crashing on 3.3.1

Alan Dodd wrote:
> Hello all,
> A recent simulation has been running on a cluster for a couple of weeks.  5.something-ns in it crashed due to a hardware glitch.  All perfectly understandable so far.
> The strange thing is, using tpbconv now results in a .tpr that crashes in the first step due to massive LINCS errors.  Even if you use the option -time to take the simulation way back, to say 0.5ns when it ought to still be fine, it still crashes.  Other simulations on the same hardware+software are running fine, other restarts from other jobs crashing at the same time have worked fine, so it doesn't look like a bug.  Any suggestions as to why LINCS errors could suddenly now prevent the simulation from running *any* of the steps that it previously ran just fine?  I just want a hint as to what we could have missed, really.
> Alan Dodd
> UoB
Did you give tpbconv the energy file as well?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,      75124 Uppsala, Sweden
phone:    46 18 471 4205        fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Luggage? GPS? Comic books? 
Check out fitting gifts for grads at Yahoo! Search

More information about the gromacs.org_gmx-users mailing list