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" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Error:Cannot determine precision of trn file > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > 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 > > [EMAIL PROTECTED] 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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