> From: davhak2...@hotmail.com > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Calculate interaction energy dynamically > Date: Thu, 25 Jul 2013 09:13:14 +0000 > > > > > Date: Wed, 24 Jul 2013 09:35:26 -0400 > > From: jalem...@vt.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > > > > > On 7/24/13 9:25 AM, Davit Hakobyan wrote: > > > Thank you again for your time and help. > > > > > > Performing "rerun" on the original system passes without warnings: > > > > > > The > > > subsequent g_energy also runs smoothly. One gets no warning also if > > > passing the ordered *ordered.tpr and the new index (*ordered.ndx) files > > > to the "mdrun -rerun" of the original system. This indeed leaves with > > > the ordered trajectory file as the only problematic point which might > > > cause the warnings. > > > > > > > Good to know. > > > > > Interestingly, the ordered *.trr file > > > (product of trjorder command) is nearly twice as small as the original > > > *.trr file. Since the coordinates in the ordered *.trr file look fine > > > then probably it is the velocities which might be missing in it. Can the > > > > There's no "might" about it - your gmxcheck output from before shows that > > velocities are definitely absent, which should account for the difference > > in > > file size. > > > > > warnings come from this issue ? In this case the g_energy should not be > > > able to calculate the kinetic energy. If this is the case may one still > > > rely on the numbers obtained by g_energy for the coulomb and vdw terms > > > (despite the warning messages) ? > > > > > > > This is a very weird issue. The .trr file clearly has step and time > > information > > (from your earlier post), but the resulting .edr file from mdrun -rerun > > does not > > have the correct step number (though it appears to have time). Your > > problem > > does not derive from anything to do with velocities, as far as I can tell. > > Proceed carefully and scrutinize the output to see if it indeed makes sense > > - > > you can verify energy values from snapshots that have not been ordered by > > creating index files that correspond to the same lipids, for instance. > > This is > > a very non-standard exercise, so it's probably never been tested and > > debugged. > > The energy calculation between the nearest neighbors at a given time frame > based on the original trajectory file (with help of new index file) indeed > gives the same values as for the ordered trajectory file. So one can probably > rely on the energy output from the ordered trajectory despite the warnings. > > In case of more information about the warnings I will write in this thread. >
It seems that the problem appears when for the trjorder command one indicates *.trr instead of *.xtc as an output. When *.xtc is mentioned like "trjorder ... -o output.xtc" both the "mdrun -rerun" and g_energy subsequently pass without warnings. > Thank you very much for all the help. > > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > ================================================== > > -- > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
