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

[David van der Spoel]

On 06/10/15 13:38, gozde ergin wrote:
> 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..
That is more or less what I expected, but the Van der Waals force do not 
mean anything without Coulomb forces. Therefore you might as well check 
the average force on all atoms.
>
> 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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-- 
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