[gmx-users] xtc corrupted during REMD
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Nov 22 13:16:29 CET 2010
On 22/11/2010 7:11 PM, andrea spitaleri wrote:
> Hi,
> two on five have magic error at the same time. The simulation ends
> fine. Just the xtc files are corrupted. The magic error is systematic,
> since I repeated the simulation 4 times and I get the same behavior
> (at different time) after the continuing run. First time, I suspected
> for some I/O error, but now it sounds a bit strange. I will ask for a
> long simulation 50ns without extending steps.
Hmm. A GROMACS code problem is most likely to be manifest by exactly
reproducible behaviour. A filesystem problem would be erratic, but
should not only occur on run extensions. You could try the continuations
with mdrun -reprod to eliminate a few GROMACS-related
non-reproducibility attributes. This is more of a diagnostic than a
long-term solution, however.
Mark
> thanks in advance
>
> regards
>
> and
>
>
> On 11/22/2010 05:44 AM, Roland Schulz wrote:
>>
>>
>> On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
>> <spitaleri.andrea at hsr.it <mailto:spitaleri.andrea at hsr.it>> wrote:
>>
>> Hi,
>> yes sure. Basically I do:
>>
>> 1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 -> i get the
>> first 5x25ns of remd simulation (five xtc every 5ps and five trr
>> every 20ps, for each replica). I check those files by gmxcheck and
>> they are fine. no errors.
>>
>> 2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 25000000 -o
>> runB_$i -> extension the simulation to 50ns total
>>
>> 3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_ ->
>> at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted
>> (from gmxcheck) whereas the trr are fine. These are from 25ns to
>> 50ns.
>>
>> >From the log file I do not see any errors. Everything seems fine.
>> I have free room space in the hd too :)
>>
>> I am just wondering whether the problem is in the xtc options
>> (precision and writing step)
>>
>>
>> I doubt it that it has anything to do with your xtc options.
>>
>> Are all you xtc corrupted or only some? Are those which are corrupted
>> all corrupted on the same frame or different ones?
>>
>> Roland
>>
>>
>> ------------------------------------------------------------
>> Andrea Spitaleri PhD
>> Dulbecco Telethon Institute
>> Center of Genomics, BioInformatics and BioStatistics
>> c/o DIBIT Scientific Institute
>> Biomolecular NMR, 1B4
>> Via Olgettina 58
>> 20132 Milano (Italy)
>> http://sites.google.com/site/andreaspitaleri/
>> Tel: 0039-0226434348/5622/3497/4922
>> Fax: 0039-0226434153
>> ------------------------------------------------------------
>> ________________________________________
>> Da: gmx-users-bounces at gromacs.org
>> <mailto:gmx-users-bounces at gromacs.org>
>> [gmx-users-bounces at gromacs.org
>> <mailto:gmx-users-bounces at gromacs.org>] per conto di Mark Abraham
>> [Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>]
>> Inviato: domenica 21 novembre 2010 17.03
>> A: Discussion list for GROMACS users
>> Oggetto: Re: [gmx-users] xtc corrupted during REMD
>>
>> On 21/11/2010 2:34 AM, Spitaleri Andrea wrote:
>> > Hi there,
>> > I am encountering a weird problem with a REMD simulation using
>> 4.5.3. The total simulation is 50ns with 5 replica, and I do in two
>> runs: 25ns and then continuing to 50ns (walltime queue). The first
>> run is okay, the continue run (the last 25ns) randomly make some xtc
>> files corrupted (from gmxcheck I get the Magic Number Error).
>>
>> I don't understand how the simulation can continue writing the .xtc
>> files when you are getting magic number errors from gmxcheck. We
>> need to
>> see command lines for your workflow, please :-)
>>
>> Mark
>>
>> > It is strange since the respective trr files are okay and the
>> simulation is still going (it is not blowing up from the log, not
>> step.pdb files, not crash). The only difference is that I am writing
>> the xtc often respect to the trr file and just the complex not the
>> solvent:
>> >
>> > nstxout = 10000 ; coordinates every 20ps
>> > nstvout = 0 ; velocity every 0ps
>> > nstfout = 0 ; forces every 0 ps
>> > nstlog = 2500 ; energies log every 5ps
>> > nstenergy = 2500 ; energies every 5ps
>> > nstxtcout = 2500 ; coordinates every 5ps to xtc
>> > xtc-precision = 2500 ;
>> > xtc-grps = complex;
>> >
>> >
>> > Since the error is happening only for the continuing run, I am
>> just wondering if there is any reason for this.
>> >
>> > thanks for any help
>> >
>> >
>> > and
>> >
>> > ------------------------------------------------------------
>> > Andrea Spitaleri PhD
>> > Dulbecco Telethon Institute
>> > Center of Genomics, BioInformatics and BioStatistics
>> > c/o DIBIT Scientific Institute
>> > Biomolecular NMR, 1B4
>> > Via Olgettina 58
>> > 20132 Milano (Italy)
>> > http://sites.google.com/site/andreaspitaleri/
>> > Tel: 0039-0226434348/5622/3497/4922
>> > Fax: 0039-0226434153
>> > ------------------------------------------------------------
>> >
>> >
>> >
>>
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