[gmx-users] RE: evb and mapping potentials

ggroenh at gwdg.de ggroenh at gwdg.de
Mon Sep 14 19:14:03 CEST 2009

>    6. EVB and mapping potentials (rsf)


I do not understand your question, but what you try to do seems interesting.

This is how far I got:

If you have only two states to interconnect, the diagonal elements would
be the energy H(lamda=0) and H(lamda=1). The off diagonals then have to be
parametrized as a function of lambda? Would diagonalization then give you
the forces on lambda?

We have a version of gromacs which supports lambda dynamics, but I am not
sure if that's what you need?



> Hi
> I want to describe a reaction for what I have a system described by two
> different connectivities and need to run an MD calculation on a mapping
> potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal
> elements of the evb matrix and C is a parameter. Does gromacs have support
> for running something like this?. Which would be the best way to run this
> calculation with the standard code, or should I modify it in order to do
> that. The states have some atoms with different connectivity between them,
> different forcefield parameters and different charges, the atom types are
> the same for both.
> Thanks for your comments.
> Romelia.
> --
> ****************************************
> Romelia Salomon
> Miller Group
> 132 Noyes
> Chemistry Department
> Caltech
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