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.
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
<[email protected] <mailto:[email protected]>> 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: [email protected]
<mailto:[email protected]>
[[email protected]
<mailto:[email protected]>] per conto di Mark Abraham
[[email protected] <mailto:[email protected]>]
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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-------------------------------
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)
Tel: 0039-0226434348
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
http://www.linkedin.com/in/andreaspitaleri
-------------------------------
-----------------------------------------------------------------------------------
SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE.
NON C'E' CURA SENZA RICERCA.
Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San
Raffaele.
Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org
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