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

Masakatsu Ito masakatsu-ito at aist.go.jp
Mon Dec 8 17:44:00 CET 2003

Thank you so much. You help me a lot to find a better way for adapting
my REMD framework to 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.
> > But if I can find out which variables of GROMACS define a box for
> > periodic boundary condition, it would be easier that my REMD framework
> > shift an atom position. 

> I'm afraid not...

I understand. It is difficult because the box for periodic boundary
condition is not geometrically simple. But I still cannot see what you
mean by the word 'charge'. 

> First, we don't shift atoms, but charge groups. 

Let us assume that, initially, all the atoms in the simulation lie
within the box. But some atoms may leave the box, as the simulation
proceeds. I think that the position shift of these atoms is enough for
getting a correct potential energy.

So, could you give me a more detailed explanation about 'charge

> > Then, does that long range correction work if I remove 
> > the update() procedure in do_md() function? 
> > And, is update() function unnecessary for calculating the potential
> > energy and force vector?
> If you use constraints you need to call update. It affects the forces
> and the pressure, but not the energies.
> It seems simplest to implement your code as another integrator in
> update. The code for the real integrators is very simple.

That would be a good idea. That integrator which I put into update()
might receive a temperature from my REMD framework.
Could you please tell me which part of update() is responsible for 
integrating equations of motion?


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

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