> Date: Fri, 26 Jul 2013 11:30:14 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Calculate interaction energy dynamically > > > > On 7/26/13 5:21 AM, Davit Hakobyan wrote: > >> 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. > > > > Interesting. That leads me to suspect that there is something wrong with the > way trjorder writes .trr frames. It writes .xtc files correctly, but > incorrect > step information in .trr files. Thanks for following up. I'll look into it > and > probably file a bug report on it. What Gromacs version are you using? Maybe > you said that before, but I've forgotten.
I use Gromacs 4.5.1. Thank you very much for your help and time. > > -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
