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

[Mark Abraham]

On 11/08/2011 1:45 AM, Da-Wei Li wrote:
> Dear Mark
>
> Could you please help me out? I can send you the trajectory (1000 
> snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3.

Not unless you can show me a shell script and .mdp file that can take 
your original trajectory, do my suggested procedure and produce your 
observed output. Otherwise, the chance of user error is a thousand times 
more likely than a GROMACS problem.

Mark

>
> I  checked the pdb file in UCSF Chimera and didn't find any crash. I 
> have about 10 snapshot that has high vdw energy.
>
> best,
>
> dawei
>
>
>
> On Wed, Aug 10, 2011 at 11:32 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     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.
>
>     Mark
>
>
>>     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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>>
>
>
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