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

[Da-Wei Li]

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.

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>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>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
>>  --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110810/2fd7b909/attachment.html>