Thanks so much Justin. With regards Debdas
On Fri, May 18, 2018 at 7:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/18/18 6:08 PM, Debdas Dhabal wrote: > >> Hi Justin, >> >> When I follow the method you suggested I am getting an error. >> (1) Using trjconv I have created a .trr file containing the coordinates of >> the component for which I want to calculate the bonded energy. >> (2) Now when I do *tpbconv_mpi -s topol.tpr (old tpr file) -f traj.trr >> (containing component of my interest) -o tpxout.tpr *, it is showing an >> error message -> "Number of atoms in Topology is not same as in >> Trajectory". >> >> This means the trr file I am supplying should contain the trajectory of >> whole system. If I do that then during *mdrun -s tpsout.tpr -rerun >> traj.trr*, >> it is giving energy for whole system not for that single component. It >> would be very nice if you could kindly help me resolving this error. >> > > There is no need for a trajectory when creating a new .tpr file - that's > an antiquated method for extending simulations. > > All you need is: > > tpbconv -s old.tpr -o new.tpr (with a suitable selection that may or may > not require an index file) > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Debdas Dhabal Postdoctoral Researcher. SEAS, Department of Chemical and Biomolecular Engineering, The University of Pennsylvania, Philadelphia, PA 19104, USA. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
