[gmx-users] Re: Calculate individual force between each atom pair

WU Yanbin ywu27 at uiuc.edu
Sun May 20 23:50:33 CEST 2007

  Thanks for the suggestions.
  I have traced the calling sequence from do_force() to calculate LJ forces:
do_force() -->force() -->do_nonbonded(). But in do_nonbonded() function of
nonbonded.c file, if for general processor, it should have call
gmx_nb_generic_kernel() function but this line is in fact commented and the
implimentation of gmx_nb_generic_kernel() can not be found. My gromacs
version is v3.3.
  So is there previous implementation of this function? I can write it
myself but the efficiency will be much lower. Any suggestions? Thanks in
                                                    Yours Sincerely,
                                                                  WU Yanbin

> Message: 4
> Date: Fri, 18 May 2007 09:14:22 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Calculate individual force between each atom
>         pair
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <464CE1CE.2090204 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> WU Yanbin wrote:
> > Hi, Everyone,
> >   The force given by .trr file is the total force acted on each atom.
> > Now I would like to modify codes to calculate individaul force between
> > each atom pair. Is it possible in gromacs? (Because I remember some part
> > of gromacs is writen in Fortran and already compiled).
> Err, no, not Fortran. The inner loops for calculating energies and
> forces are written in assembly for some common architectures, and there
> are fall-back routines in C. It would not be too hard to modify these C
> routines to write the nonbonded force between pairs of atoms in the
> inner loops. Writing that to output is likely to be unreasonably slow,
> and generate an unreasonably large data size (it's effectively a
> trajectory of size N^2 now). Depending on your application you might not
> need to write the numbers to a file, but you haven't told us what you
> want here.
> In any case, think very carefully about what you want to do, and then be
> prepared to understand the whole structure of mdrun, and lots of fine
> detail inside do_force()
> Mark
> ------------------------------
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