Dear all,

I would like to bring up the issue of calculations
or separation of the
solute-solute and solute-solvent interaction energies
in the course of MD. This is essential if one wants to
compute, for example, free energy. The way I discussed with
Dr.Refson seems not efficient in moldy and the simple approch
might not be complete. There are somethings like distance potential
(dist_pot) as well as Ewald to be taken into account (or not).

Looking forward to your comments

Kritsana Sagarik
****** Forwarded Message Follows *******

Dear Dr Sagarik,


 > I am a moldy user with not much experience in C programming. I am
 > a FORTRAN programmer.

If you are not sure of writing C code, it's really quite easy and
there should be a straightforward map to fortran. write y

 > We are interested in MD simulations on solute-solute,
 > solute-solvent and solvent-solvent interactions. I noticed that the
 > potential energy is computed at "site" identified by id[isite].

It is not true that this array contains the potential energy per
site. To avoid double-counting it only contains a subset and only the
sum is the total physical PE.

 > So if I
 > want to compute the interaction energy between a solute, with site id 1-10,
 > with water molecules, with site id 11-14, I simply sum up the potential at
 > site 1-10 (pe).
 > I think that doing this might decrease the performance of moldy.
 > Please give me a better approach.

I'm afraid I don't have a general approach to this.  Perhaps if you
were to explain your question fully on the moldy email discussion list
you might find someone who has already thought about this problem.

sincerely

Keith Refson
--
Dr Keith Refson,
Building R3
Rutherford Appleton Laboratory
Chilton
Didcot
Oxfordshire OX11 0QX
T: 01235 446652         K.Refson@
F: 01235 445720         @rl.ac.uk