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
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