On Fri, Mar 15, 2013 at 7:10 PM, Alexander Peyser <[email protected]>wrote:
> Dear all, > > I'm receiving a "timesteps don't match" error, due to a wobble in the time > between steps for my xtc trajectory file. The source of the wobble is > mysterious. > > I'm running gromacs-4.5.5 with plumed patches for a very long trajectory > using double precision code with a time step of 2fs and xtc frames every > 200fs. The trajectory was run in 24 hour chunks, with a continuation with > -append over all the chunks. The timing fit precisely the values set over > many, many chunks. > > Unfortunately, I was trying to consolidate some disk space and lost my log > file, which kept me from simply running mdrun_d with -append to continue > the trajectory as I had been doing. I started a new trajectory with the > checkpoint file by extending the tpr with tpbconv, and then continued > appending to the output from that. The beginning time is correct, beginning > right after the end of the first trajectory. However, every frame is > separated from the next by 187.5 fs or 218.75 fs, repeatedly. I've checked > my input files, my cpt checkpoint and my tpr run file --- there are no step > values like that at all, and the xtc output time continues to be set as > every 100 steps, with a step time of 2fs. > > Where should I look to identify the source of this wobble? Has anyone seen > anything similar? > Sounds pretty weird. I haven't got any theories on how that could happen. If you've got input files that can reproduce the issue, please file it on redmine.gromacs.org. Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
