[gmx-developers] calculate the potential...

[Daniele Bemporad]

Hi Giorgos
The potential energy is stored in individual variables for each 
component of the potential energy function (bonds, angles, dihedrals, 
LJ, Coul, ...) and their name depends on the subroutine. However the 
names are always something like v, va, vtot... and the total potential 
energy (the sum of all the above components) is in etot or something 
similar.
Daniele

On Thu, 8 May 2003, Giorgos Karvounis wrote:

> 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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