[gmx-developers] Interface - energy value from peptide conformation

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Fri Sep 24 10:22:07 CEST 2010


I just started experimenting with GROMACS and I would like to interface with
it to get energy values for different conformations of peptides. When
debugging my way through the energy minimization part of the gmxdemo
tutorial, I ended up in the following method of the mdlib/minimize.c file:

static void evaluate_energy(FILE *fplog,bool bVerbose,t_commrec *cr,
    t_state *state_global,gmx_mtop_t *top_global,
    em_state_t *ems,rvec **buf,gmx_localtop_t *top,
    t_inputrec *inputrec,
    t_nrnb *nrnb,gmx_wallcycle_t wcycle,
    gmx_vsite_t *vsite,gmx_constr_t constr,
    t_fcdata *fcd,
    t_graph *graph,t_mdatoms *mdatoms,
    t_forcerec *fr, rvec mu_tot,
    gmx_enerdata_t *enerd,tensor vir,tensor pres,
    int count,bool bFirst)

I'm not very experienced with C/C++, but the fact that this method is static
means that I cannot just call it from another C program (or e.g. a Java
program) without changing GROMACS. I guess a naive way would be setting up
an energy minimization and just running one step, but that is a lot of
overhead and not very clean. Do you have any pointers for me?

(Actually, what I want to do is navigate the energy landscape of peptides by
changing the torsion angles. This means that I will need to look up energy
values very frequently.)

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