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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 10 17:32:16 CEST 2011

On 11/08/2011 1:18 AM, Da-Wei Li wrote:
> 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.

If all you've done is strip water, make molecules whole with trjconv 
-nojump from a reference configuration that had whole molecules, and use 
pbc = no in the .mdp file, then that sounds impossible.


> best
> dawei
> On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto: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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