Are you running out of disk space? What does gmxcheck tell you about these .trr files?
-Justin Quoting [EMAIL PROTECTED]: > Hi all, > I have been trying to simulate octa-alanine peptide in a mixed solvents > like as mentioned below on Cluster of 128 nodes. > 1. water, Trifluoroethanol > 2. water, Guanidium ion, Chloride ion > > simulation was going on properly till 26 ns.I have extended simulation to > 50 ns.simulation runs properly but when i started to analyze by > ngmx -f *.trr -s *.tpr > ngmx shows some parts of trajectory not completely & then it gets crash > with the following message > > > ****************************************************************************** > Program ngmx, VERSION 3.3.3 > Source code file: ../../../../src/gmxlib/trnio.c, line: 66 > > File input/output error: > Can not determine precision of trn file > ****************************************************************************** > > > And when i started to extend the simulation for more time with > tpbconv -s x.tpr -f x.trr -o new.tpr -until 100000 > it wouldn't be able to generate new.tpr file for extended run.it pop-up > the message as below... > *************************************************************************** > Program tpbconv, VERSION 3.3.3 > Source code file: ../../../../src/gmxlib/trnio.c, line: 66 > > File input/output error: > Can not determine precision of trn file > **************************************************************************** > Earlier i was not facing this problem for extending the simulation.I > again started with fresh previous run i.e starting from 26 ns simulation > runs and when it get stopped i tried both ngmx & tpbconv the same > message have come but at different time steps. > I am not getting what's happening. > > I am waiting for positive response.... > > with warm Regard > Kinshuk > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
