Hi Dmitri, Try
editconf -f your_run_input_file.tpr -o test.gro to see if the box is stored correctly in the .tpr. Alternatively, you can do gmxdump -s your_run_input_file.tpr, and browse for the box in the output. Then, see if you can reproduce the problem with the last frame of the .trr file extracted, and consider submitting a bugzilla. Cheers, Tsjerk On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov <[email protected]> wrote: > First, sorry for the revival of this thread so late (maybe it should be > better to start a new one). > >> ----- Original Message ----- > >> From: Dmitri Dubov <[email protected]> > >> Date: Thursday, May 27, 2010 19:11 > >> Subject: Re[2]: [gmx-users] Non-conservation of total energy while > >> using structure file to resume the simulation > >> To: Discussion list for GROMACS users <[email protected]> > >>> > I expect that either > >>> > grompp -f new -o newtpr > >>> > mdrun -s newtpr -cpi old_state.cpt > >>> No, this way is unsuccessful, maybe due to somewhat contradictive >>> instructions: > >>> grompp supplies newtpr with usual options > >>> tinit = 0 > >>> nsteps = 100000 > >>> simulation_part = 1 > >>> and from old_state.cpt the system finds itself on 100000th step already >>> and stops. > >> OK. Presumably some more cunning choice of .mdp options would work, > >> or using grompp, tbconv -extend and then mdrun. > >>> > grompp -f new -t old_state.cpt -o newtpr > >>> > mdrun -s newtpr > >>> > will do what you want. Please report back if one or both work :-) > >>> And the latter variant is working! More precisely I use > >>> grompp -f new -t old_state.cpt -c oldtpr -o newtpr > >>> mdrun_d -s newtpr > >> Mark > > But I have noted just now that using grompp with -t option results in some > bug: after simulation right size of my cubic box (last line of input > structure file) > > 10.00000 10.00000 10.00000 > > changes in confout.gro to meaningless > > 0.00000 0.00000 0.00000 > > To analyse the output properly (e.g. with g_rdf tool) I have to correct this > line manually. > > And I'm worried whether this bug effects to my simulation itself, during md > integration of NVE ensemble in vacuum? > > -- > > Rerards, > > Dmitri mailto:[email protected] > > -- > gmx-users mailing list [email protected] > http://lists.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. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.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
