[gmx-users] strange vdw energy from rerun with GBSA model.
lidawei at gmail.com
Wed Aug 10 16:29:54 CEST 2011
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.
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?
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