[gmx-users] strange vdw energy from rerun with GBSA model.
Mark.Abraham at anu.edu.au
Wed Aug 10 17:32:16 CEST 2011
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.
> On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at 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
> I believe fitting or no-jump processing shall not change the
> energy at all.
> Any one has idea about this?
> As above.
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