Hi, You may have written only a subset of atoms to the new trajectory files using trjconv. Keep track of what you're doing and what is in which file. Besides, most analysis tools also accept .pdb/.gro files for reference.
Cheers, Tsjerk On Feb 15, 2008 6:31 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > > " Molecule in topology has atom numbers below and above natoms. you are > > probably trying to use a trajectory which does not match the first 330 atoms > > of the run input file. You can make a matching run input file with tpbconv." > > Use the same .tpr file that you submitted to mdrun to generate the trajectory. > It has the reference structure for your simulation (t=0). Try with -pbc > nojump > and -pbc whole to see which reconstructs your system appropriately. > > -Justin > > > > > with regards > > Anamika > > > > > > ======================================== > > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
