Dear Mark Could you please help me out? I can send you the trajectory (1000 snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3.
I checked the pdb file in UCSF Chimera and didn't find any crash. I have about 10 snapshot that has high vdw energy. best, dawei On Wed, Aug 10, 2011 at 11:32 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 11/08/2011 1:18 AM, Da-Wei Li wrote: > > Dear Mark > > That is my thought too.To test this possibility, I created a mdp file > without PBC and use trjconv -pbc nojump to make whole protein. >From > visualization in UCSF Chimera, the trajectory looks fine. But I still have > some snapshot that have very high vdw energy. > > > If all you've done is strip water, make molecules whole with trjconv > -nojump from a reference configuration that had whole molecules, and use pbc > = no in the .mdp file, then that sounds impossible. > > Mark > > > best > > dawei > > On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 11/08/2011 12:29 AM, Da-Wei Li wrote: >> >>> Dear Gromacs users: >>> >>> I recently tried some MM/PBSA stuff using the rerun function of mdrun and >>> GBSA model. All water molecules are stripped off the trajectory file. >>> >>> However, when I examine the different energy term, it is disturbing that >>> short range vdw energy of some snapshot are very high (> 1000 kj/mol) while >>> others snapshots typically have a value around -2000 kj/mol. >>> >> >> Something is badly wrong - perhaps your treatment of periodicity in the >> rerun - but we don't have anywhere near enough information to know. >> >> >> >>> It is more disturbing that if I do a fitting or pbc nojump on the >>> trajectory first, I will get very different short range vdw for some of the >>> snapshots. All other energy terms are un-affected. >>> >>> I believe fitting or no-jump processing shall not change the energy at >>> all. >>> >>> Any one has idea about this? >>> >> >> As above. >> >> Mark >> -- >> 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