[gmx-users] Van der Waals force extraction in Gromacs 5.0

gozde ergin gozdeeergin at gmail.com
Tue Oct 6 13:38:55 CEST 2015


I just want to extract the van der Waals forces between the atoms in my
system.

I have system that covers water + organic molecules. As organics I am using
5 different kind of molecules like 1-decanol(straight),
iso-decanol(branched),1-decanol248trimethyl(more branched) .
To understand the branching effect on the system I would like to extract
van der waals forces of each system..

On Tue, Oct 6, 2015 at 1:32 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 06/10/15 12:08, gozde ergin wrote:
>
>> Thank you Mark but I could not understand how to do a 'suitably hacked
>> .tpr' in order to get the vanderwaals forces.
>>
>
> It would be good to explain briefly what you are trying to achieve as a
> courtesy to the people answering questions.
> There may be better alternative ways to achieve things.
>
>
>> On Tue, Oct 6, 2015 at 11:57 AM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> No. Force components are never stored. You might be able to use mdrun
>>> -rerun with a suitably hacked .tpr to get what you want.
>>>
>>> Mark
>>>
>>> On Tue, Oct 6, 2015 at 11:34 AM gozde ergin <gozdeeergin at gmail.com>
>>> wrote:
>>>
>>> Dear users,
>>>>
>>>> Is there way to extract only van der Waals forces from trajectory in
>>>> Gromacs 5.0?
>>>>
>>>> Thanks in advance
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> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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