[gmx-users] Which variable represents the potential energy ?

[David]

On Fri, 2003-12-05 at 19:59, masakatsu-ito at aist.go.jp wrote:
> Hi,
> 
> I am trying to make another implementation of replica exchange method
> (REM) which calls gromacs code for calculating potential energies.
> However, my program still does not work because the potential energy
> at each step becomes zero.
> 
> I assumed that do_force() function calculates the potential energy,
> and ener[F_EPOT] variable in this function represents the potential
> energy. But I found that ener[F_EPOT] is zero after calling do_force()
> in both my REM program and mdrun.

it is computed a little later in sum_epot.


> 
> So could please anybody tell me which argument of do_force()
> represents the potential energy ? This function has a argument list
> like
> 
>   FILE *log, t_commrec *cr, t_commrec *mcr,
>   t_parm *parm,t_nsborder *nsb,tensor vir_part,tensor pme_vir,
>   int step,t_nrnb *nrnb,t_topology *top,t_groups *grps,
>   rvec x[],rvec v[],rvec f[],rvec buf[],
>   t_mdatoms *mdatoms,real ener[],t_fcdata *fcd,bool bVerbose,
>   real lambda,t_graph *graph,
>   bool bNS,bool bNBFonly,t_forcerec *fr, rvec mu_tot,
>   bool bGatherOnly
> .
> 
> Or should I call another function to get the potential energy?
> 
> Thanks a lot in advance.
> Masakatsu
> 
> Masakatsu Ito , Ph.D
> 
> Grid Technology Research Center
> National Institute of Advanced Industrial Science and Technology
> Tsukuba Central 2, Tsukuba, Ibaraki 305-8568 Japan
> Phone : +81-29-861-5730  Fax : +81-29-861-5301
> E-mail masakatsu-ito at aist.go.jp
> URL http://met.sourceforge.net/
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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