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-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Jan 24, 2012, at 8:23 PM, Sidney Elmer <paulymer.gmail.com> wrote: > Thanks Bill, > > After I sent the first email, I remembered that it is possible to dump > multiple restrt files as you mentioned; just add a minus sign to the > argument of ntwr, e.g. ntwr = -1000. I thought of doing that, although it > is not as clean as having all the frames saved in a single trajectory file. > But having a hundred restrt files with the velocities output automatically > sounds much more preferable than having to manually compose the restrts > with the velocities. Is there any talk of making the following workflow, > umm, work? > > 1. save coords and velocities both in the same netcdf file with the mdin > options "ioutfm = 1, ntwv = -1, ntwx = 100" > 2. to subsequently print out individual restart frames (with > velocities), just give ptraj the following commands: > trajin mdcrd > trajout <framename> restart > go > > It seems like this should be a standard workflow, rather than having to > deal with the other workarounds each of us has suggested. Thanks for the > help. > > Sid > > On Tue, Jan 24, 2012 at 4:29 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >> To get velocities to match mdcrd, you need to save mdvel as well, >> then manually compose restrts from corresponding frames of mdcrd/mdvel. >> Note that these will truncate precision so won't be as fully equilibrated >> as the trajectories they came from. This is true to a lesser degree for >> non-netcdf restrts, since they have less precision than the binary >> format. >> >> Once upon a time there was talk of an option to dump multiple restrt >> files during the trajectory, not sure what the status of that is. >> >> Bill >> >> Sidney Elmer <paulymer.gmail.com> wrote: >> >>> Hi, >>> >>> I set up my simulation with the following flags: ioutfm = 1, ntwv = -1, >>> with the expectation that I would be able to pull restart files from any >> of >>> the frames saved in the mdcrd file. However, when I output the frames >> into >>> individual restart files using ptraj: >>> >>> trajin mdcrd >>> trajout frame restart >>> go >>> >>> >>> all of the velocities are 0.000000. Did I do something wrong? How do I >>> get the restart files with the velocities as I was expecting? Thanks for >>> your help. >>> >>> Sid >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Jan 24 2012 - 21:00:02 PST