[gmx-users] New force fields
Ram'on Garc'ia Fern'andez
ramon at jl1.quim.ucm.es
Sat May 4 00:18:29 CEST 2002
On Fri, May 03, 2002 at 09:59:47AM -0700, Erik Lindahl wrote:
> >Although not needed for supporting other force-fields, one feature that
> >I find essential is the capability of using different potentials for
> >different atom types. At present all the atom types must use the same
> >potential, albeit with different parameters.
> Yes, we should definitely add this as a formatting option to the force
> fields, but it will be much
> more difficult to actually implement it. The main problem is what we
> should do with the cross
> terms; If atom A uses LJ and atom B Buckingham, what do we do with the
> A-B interaction?
I do not understand why there is a problem. In that case, either the user
has defined a specific potential for the pair A-B; otherwise grompp give
an error message.
> >In addition, the procedure for adding a custom potential (that is, with
> >a different formula) should be documented (as opposed to adding a potential
> >defined by a table, that is well documented). More that two parameters
> >should be allowed.
> I've been thinking of that; It's not too hard to document it, although
> some of the code in the
> innerloop generator could use a little cleaning-up. One problem is of
> course that your code
> would only be C or Fortran (never SSE/SSE2/3DNow or Altivec assembly),
> so you would lose
> a significant amout of speed (say ~40% of your performance). Since the
> table loops are
> written in assembly they will always be faster when you can use them.
Well, that is up to the user to choose.
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