[gmx-users] strange vdw energy from rerun with GBSA model.
lidawei at gmail.com
Wed Aug 10 17:45:11 CEST 2011
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.
I checked the pdb file in UCSF Chimera and didn't find any crash. I have
about 10 snapshot that has high vdw energy.
On Wed, Aug 10, 2011 at 11:32 AM, Mark Abraham <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.
> 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
>>> Any one has idea about this?
>> As above.
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