[gmx-developers] Regd. Changing force calculation
spoel at xray.bmc.uu.se
Thu Jun 26 10:23:51 CEST 2003
On Thu, 2003-06-26 at 10:06, Daniele Bemporad wrote:
> Hi Anjan
> If I understand correctly your e-mail, you want to use something else
> than the standard potential energy terms in gromacs. When running mdrun
> (I have no clue for other types of calculations, e.g. minimization), you
> use subroutine do_md (in file src/kernel/md.c) which calls do_force (in
> src/mdlib/sim_util.c) which in turn calls force (in file
> src/mdlib/force.c). I would say this is the key subroutine. It calls
> calc_bonds (which calculates the bonded interactions, in file
> src/gmxlib/bondfree.c) and do_fnbf (which calculates the non-bonded
> interactions, in file src/gmxlib/fnbf.c). The latter uses the inner
> loops, some of which written in assembly and some others written during
> the compilation by src/gmxlib/mkinl*.c files. If you want to modify the
> potential energy function, then either modify the above subroutines or
> disable them and write your own for instance inside force.c.
> Corrections/comments from the authors of the program are wellcome.
this is correct. Furthermore it depends on what you would like to add.
> Hope this helps.
> On Wed, 25 Jun 2003, Anjan Raghunathan wrote:
> > Hi,
> > I'd like to know which function(s) to modify if I need to
> > use a separate force calculating(and potential) function of my
> > own at every timestep in GROMACS. Could anyone point out the
> > functions that are this particular force function call
> > dependent and which function I should modify?
> > thanks,
> > Anjan
> > _______________________________________
> > Anjan V. Raghunathan
> > Graduate Research Assistant
> > Computational Electronics Group
> > 3213 Beckman Institute,
> > Univ. of Illinois at Urbana-Champaign.
> > E-mail:araghuna at uiuc.edu
> > Off: 217-244-1964
> > Res: 217-355-5418
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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