[gmx-developers] external potential ?

Gerrit Groenhof G.Groenhof at chem.rug.nl
Wed Feb 11 12:34:39 CET 2004

Hi Michael,
In force.c

At any point you can add a force on the particles in the
force function (src/mdlib/force.c)
The particles' forces are in f[], the positions in x[]. Furhter you
might need to acces the mdatoms struct, containing the info
of the particels in the simulation.

So the simplest in my opinion would be something like:

in void force(FILE       *fp,     int        step,
	   t_forcerec *fr,      t_inputrec *ir,
	   t_idef     *idef,    t_nsborder *nsb,
	   t_commrec  *cr,      t_commrec *mcr,
	   t_nrnb     *nrnb,
	   t_groups   *grps,    t_mdatoms  *md,
	   int        ngener,   t_grpopts  *opts,
	   rvec       x[],      rvec       f[],
	   real       epot[],   t_fcdata   *fcd,
	   bool       bVerbose, matrix     box,
	   real       lambda,   t_graph    *graph,
	   t_block    *excl,    bool       bNBFonly,
	   matrix lr_vir,       rvec       mu_tot,
	   real       qsum,     bool       bGatherOnly)

  for (i = 0;i<md->nr;i++) /* t_mdatoms *md comtains the info see
	                      mdatoms.h in include/types 
       check_for_some_criterium(x, ...)
       for(j=0;j<DIM;j++) /*DIM = 3, the number of dimensions*/



Good luck,


> Dear all,
> Can I apply an external potential (possibly tabulated) acting on
> all particles in my simulation box, e.g. a kind of PMF (f(z))
> to represent a surface ?
> If not, where in the source-code would be the best place
> to implement such an external potential ?
> cheers,
> Michael
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