[gmx-users] Re: gmx-users Digest, Vol 51, Issue 32

[Justin A. Lemkul]

This type of error is tough to diagnose.  Maybe the system behaved 
strangely (looks like it might be imploding), or maybe there was a 
hardware problem that caused a blip in the system.  I don't know of a 
fix for this problem, so I guess it's up to you to investigate whether 
it was the simulation or the hardware that was the problem. 

You can probably use trjconv to carve out the usable frames (up to about 
t = 200 ps, it appears) to see if your system is imploding; that may be 
useful in solving the issue.

-Justin

plmallip at mail.uh.edu wrote:
> thankyou Justin for your response. The gmxcheck output is as follows
>
> Reading frame     180 time  180.000  
> Reading frame     190 time  190.000  
> Reading frame     200 time  200.000
> |
> |
> Distance between atoms 2208 and 2210 is 0.000, should be 0.136
> Distance between atoms 2208 and 2209 is 0.000, should be 0.123
> |
> |                           
> Distance between atoms 8864 and 8867 is 0.000, should be 0.100
> Distance between atoms 8864 and 8866 is 0.000, should be 0.100
> |
> |
> -------------------------------------------------------
> Program gmxcheck, VERSION 3.3.3
> Source code file: ../../../src/gmxlib/trnio.c, line: 66
>
> File input/output error:
> Can not determine precision of trn file
>
> trjconv output is
>
> Will write xtc: Compressed trajectory (portable xdr format)
> trn version: GMX_trn_file (double precision)
> Reading frame       0 time    0.000  
> Setting output precision to 0.001 (nm)
> ------------------------------------------------------- time  
> 570.000     
> Program trjconv, VERSION 3.3
> Source code file: trnio.c, line: 66
>
> File input/output error:
> Can not determine precision of trn file
> -------------------------------------------------------
>
> Is the system crashing after running for a while? Is there anyway, I 
> can use the .trr result or do I need to give mdrun again?
>
> Thanks & regards,
> Prema.
> >
> > Message: 1
> > Date: Mon, 07 Jul 2008 20:49:00 -0400
> > From: "Justin A. Lemkul" <jalemkul at vt.edu>
> > Subject: Re: [gmx-users] Error:Cannot determine precision of trn file
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <4872B97C.7030401 at vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > What does gmxcheck tell you about these .trr files?
> >
> > Also, it is better to give exact command lines with copy-pasted
> > screen
> > output, instead of leaving us to guess at what you're trying.
> >
> > -Justin
> >
> > plmallip at mail.uh.edu wrote:
> > > Dear colleagues,
> > >
> > >                   I successfully finished a 3 ns gromacs run using 40
> > > nodes.  When, I tried to convert .trr file to .xtc using
> > trjconv, the
> > > run stops at 560 frame giving error "cannot determimine
> > precision of
> > > trn file". I tried various options like -skip, -b and -e, -dt
> > option
> > > as well as -ndx option . But, each time, the run stops at 560.
> > >                 The second run I gave for 6 ns and this time, the
> > > trjconv stops at 1180 frame. I have observed the .trr files
> > occupying
> > > huge memory space - 18 G for 3ns and 34 G for 6 ns runs
> > respectively.
> > > Memory is not a problem, as I have lot of disk space available.
> > >       My system is a pentamer
> > with 1052 residues and 47201 water
> > > molecules.The simulation ran for 5 days.
> > >
> > > I would be extremely thankful for any kind of suggestions in
> > this regard.
> > >
> > > Prema,
> > > Graduate student,
> > > University of Houston.
> ------------------------------------------------------------------------
>
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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