[gmx-developers] calculate the potential...

[David]

On Thu, 2003-05-08 at 19:08, 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! 

The potential is printed after every step in the energy file. Unless you
mean the electrostatic potential which is not saved.
> 
> 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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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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