[gmx-users] strange vdw energy from rerun with GBSA model.

Da-Wei Li 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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