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

Da-Wei Li lidawei at gmail.com
Wed Aug 10 17:18:27 CEST 2011

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.



On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham <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 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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