Hi, On Sunday, 15. June 2008 18:12, sudheer babu wrote: > I am having the evidence that I have drawn RMSD plot for 7.25ns > simulation, in rmsd.xvg file showed the values of the time(ps), > mentioned in *trjconv command > > Im pasting my .mdp file > > title = dpt_prod > constraints = hbonds > integrator = md > dt = 0.002 > nsteps = 500000 > nstcomm = 1 > > ;output control statements > nstxout = 100 > nstlog = 100 > nstenergy = 100 > nstlist = 10 > ~ > ~ > > My idea of doing this trjconv command is by mistaken I have deleted > 7thns .trr but I have that file in .xtc format, so I am trying to get > 7ns file in .trr format for continue my simualation
see http://wiki.gromacs.org/index.php/Doing_Restarts If you lost your trr file you can`t do exact restarts. The xtc file has no full precision information which would be therefore necessary. Also you should upgrade gromacs to version 3.3.3, i think there s this xtc bug fixed. > > Thanks in advance. > > sudheer babu wrote: > >* Hi all, > > *>* I am having 7.25ns trajectory file , I am trying to pick up > *>* 6250ps to 7250 ps trajectory file from whole trajectory by using > trjconv, *>* Command line is > *>* *trjconv -f 7.25ns.xtc -s pr.tpr -o 6.25_7.25_out.trr -b > *>* 6250 -e 7250 > *>* selected " system " for getting output > *>* it showed the following error > *>* ----------------------------------------------------------------- > *>* Program trjconv, VERSION 3.3.1 > *>* Source code file: trxio.c, line: 635 > *>* > *>* Fatal error: > *>* Specified frame doesn't exist or file not seekable > *>* ----------------------------------------------------------------------- > * > > >That sounds pretty specific to me. What's your evidence that the file is > >seekable and these frames exist? > > > >Check that your .mdp file options should have caused XTC output to be > >written in this time. Then look at a gmxdump of this .trr file. > > > >It's not relevant to the problem, but there's almost no value in writing > >XTC input in .trr format on output. > > > >* I have found few discussions in gmx-archives regarding this problem and > > *>* due to BUG in source code its showing error. > * Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-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
