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

masakatsu-ito at aist.go.jp masakatsu-ito at aist.go.jp
Sun Dec 7 19:02:01 CET 2003

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

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().

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?

I would appreciate any hints.


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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