[gmx-users] cannot determin precesion of .trn file
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 10 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 listgmx-users@gromacs.org 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
Re: [gmx-users] cannot determin precesion of .trn file
[EMAIL PROTECTED] wrote: 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 10 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 You probably have very positive energies. with warm Regard Kinshuk ___ gmx-users mailing listgmx-users@gromacs.org 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] cannot determin precesion of .trn file
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 10 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 listgmx-users@gromacs.org 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 listgmx-users@gromacs.org 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
