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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 10 17:12:01 CEST 2011

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.


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