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

[David]

On Mon, 2003-12-08 at 17:43, Masakatsu Ito wrote:
> 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.
Gromacs already does that, every time that neighbor searching is done
(see sim_util.c)
> 
> So, could you give me a more detailed explanation about 'charge
> groups'?

It is described in the manual.

> 
> > > 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?
> 
Look for routine like do_update(), make a copy of that and rename and
edit it.


> 
> Regards,
> 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
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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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