[gmx-developers] calculate the potential...

Giorgos Karvounis gk237 at cam.ac.uk
Thu May 8 19:08:20 CEST 2003

Dear Daniele,

thanks for the reply. I looked for those files and i found the functions. I
see that both do_fnbf and calc_bonds take the force variable( rvec  f []) as
an argument so i assume that the force is calculated inside those functions
and then sum it up later (right ...???). You also put  the coordinates (rvec
x[]) as an argument , i assume you have to use that in order to calculate the
force analytically.
I am interested in the actual potential before you compute the derivative
...and i have to say that i am still struggling to trace it ... i know that
maybe i am asking too much but if you can remember (or trace) the actual
variable that holds the potential or the function that holds the derivative it
would be a great help!

Thanks again

Daniele Bemporad wrote:

> Hi Giorgos
> I cannot remember now the exact names of the variables, but I can tell
> you this:
> do_md (in file md.c) calls do_force (in sim_util.c),
> do_force calls force (in force.c),
> force calls do_fnbf (in fnbf.c) for LJ and Coulombic and calc_bonds (in
> bondfree.c) for bonds, angles and dihedrals. Remember there is a part of
> the code written in assembler.
> Daniele
> On Thu, 8 May 2003, Giorgos Karvounis wrote:
> > Dear developers,
> > The forces are the negative derivatives of a potential function V (r1,
> > r2, . . . , rN)...
> > i want to hack the code and save this potential but at the moment i find
> > difficult to trace the file...
> > While i am still looking at the archives, i would be grateful if you
> > could tell me which file contains the calculation of the force ... i
> > also assume that there is a variable (maybe structure) that holds the
> > sum of all the potentials ... can you please tell me which variable to
> > look for?
> >
> > Thank you in advance
> >
> > Giorgos
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