[gmx-users] Forces

[David van der Spoel]

On Thu, 25 Jul 2002, K.A. Feenstra wrote:

>> 
>> In the mdp options file, the nstfout is switched on and the total force
>> acting on each atom is written out in the trajectory file. I would like to
>> separate this total force into the internal forces (between the atoms of
>> the solute) and the external forces (between the atoms of the solute and
>> the atoms of solvent). Is there any option in GROMACS or will I have to
>> change something in the force subroutine? Thanks.
>
>No, there is no option (or default analysis tool) for it in Gromacs.
>However, if I'm not mistaken you can use g_traj to extract the
>force values from your trajectory and write it in ascii format,
>so you could write a simple program or script yourself. Alternatively,
>you can write a c-program using the template file that is provided
>somewhere in the gromacs source tree.
>
>You will in any case not need to modify the force subroutine, as 
>all you would want is already present in the trajectory...

Actually I think that's not correct. He wants the the solute-solute forces
and solute solvent forces. This is not possible simply, but maybe by
rerunning the trajectory (mdrun -rerun) it can be done:
use trjconv to select only the solute out of your trajectory and rerun
that, then you subtract those force from the total forces on the solute
atoms (from the original trajectory) and you have your result. It is a bit
tedious, but should work fine.

>
>-- 
>Groetjes,
>
>Anton
> ________ ___________________________________________________________
>|        | Anton Feenstra                                            |
>| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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>| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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