Hi, Tsjerk. Thanks for your help.
> 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. Yea, both tests show "zero" box right in .tpr file! > Then, see if you can reproduce the problem with the last > frame of the .trr file extracted, I'm afraid I cannot do it quickly... For the future: I used double-precision mode, how much should be the precision (-ndec) of the extracted frame? > and consider submitting a bugzilla. Sure. > Cheers, > Tsjerk > On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov <ddu...@ngs.ru> 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 <ddu...@ngs.ru> >>> 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 <gmx-users@gromacs.org> >>>> > 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? -- Regards, Dmitri
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php