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

[plmallip at mail.uh.edu]

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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