[gmx-users] indexing atoms *Altering code

[David van der Spoel]

toma0052 wrote:
> Hi,
>      Thank you for the response.  Being that Fortran is much more my
> language of choice than C, I was wondering if someone could point me in the
> right direction as far as modifying the C code to do what I want.  It is my
> understanding that an mdrun begins by making a neighbor list, computing the
> forces, globally summing the forces, and then updating the positions and
> velocities.  So I am assuming that, just after globally summing the forces,
> I can run an if statement  over all of the solvent molecules testing
> whether their z-coordinate is within certain bounds, and if so, simply add
> Fsum = Fsum + Fext.  My question is, where do I do this?  Do I have to do
> it in multiple files?  Where are those files stored in Gromacs?  Is it the
> mdrun.h and force.h files that I need to modify?  Sorry if this should be
> obvious, but again, my C skills are not the best.
> 
Go to src/mdlib/sim_util.c
Look at the code in function efield (electric field).
If your external force is just a function of the Z coord you can make a 
similar function that you call straight after the electric field 
function is called.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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