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

[David]

On Sun, 2003-12-07 at 19:00, masakatsu-ito at aist.go.jp wrote:
> Hi, David.
> 
> Thanks to your advice, my REM program seems to work well.  My REMD
> program, however, is not yet completely implemented, because I still
> cannot find a way to deal with an integrator in update() function of
> GROMACS.
> 
> So I am trying to use my code instead of update() for integrating
> EOM. That is, my REMD framework would pass the atom positions to
> do_force() function of GROMACS, and would receive the the potential
> energy and force vector.  Then my framework integrates equations of
> motion with the Gaussian thermostatting technique.
> 
> Now I am writing an adaptor function which transmit the atom positions
> and transfers the potential energy and force vector.  Most of this
> adaptor code is taken from do_md() function.
> 
> So I have a favor to ask of you and any of GROMACS people.  Would you
> kindly tell me which part of do_md() is responsible for dealing with
> the periodic boundary condition? I think I have to shift an atom
> position when the atom happens to cross the boundary of a box. But I
> cannot find which function shift atom positions in do_md().

part of it is in force.c 
part of it is in update.c

I doubt whether your code should be doing any PBC. Why do you think
that?

> The other question is about sum_epot(). Would you kindly tell me why
> sum_epot() is not called immediately after calling do_force() in
> do_md() function? Should I call another function between do_force()
> and sum_epot() to get the potential energy?
> 
because there are corrections which depend on virial (long range
corrections) which should be summed first, in particular when running in
parallel


-- 
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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