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.
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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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