[gmx-users] Forces

[Nguyen Hoang Phuong]

> > 
> > Dear All,
> > 
> > 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.

Dear Anton,

you are right. However, the force values in the  trajectory file is the
total force acting on each atom. I would like to know the internal forces:
bond stretch, torsion angles, bond angles, LJ force, Coulomb force between 
atoms of the solute and the external force: between atoms of the solute
and the  solvent. These forces should be computed in GROMACS for every
time step. However I do not know how to output these at every
step. I have spent a lot of time to look at the source codes but I haven't
found yet where to do.  

Thank you very much for any help in advance.

Regards,

Phuong

> 
> You will in any case not need to modify the force subroutine, as 
> all you would want is already present in the trajectory...
> 
> 
> -- 
> Groetjes,
> 
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
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> 
> 
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