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
advance.
Yours Sincerely,
WU Yanbin
------------------------------
Message: 4
Date: Fri, 18 May 2007 09:14:22 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Calculate individual force between each atom
pair
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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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