[gmx-developers] constraints and BAR free energy
floris_buelens at yahoo.com
Wed Oct 20 10:51:12 CEST 2010
I have a question about the perturbation of constraints. My understanding is
that dv/dlambda is easily calculated for constraints, so that constraint
perturbation is fine for thermodynamic integration - but that calculating the
deltaV to another lambda value as required for e.g. BAR doesn't make sense or
isn't practical. Here's the relevant comment in force.c:
/* Notes on the foreign lambda free energy difference evaluation:
* Adding the potential and ekin terms that depend linearly on lambda
* as delta lam * dvdl to the energy differences is exact.
* For the constraint dvdl this is not exact, but we have no other option.
So far I've always avoided perturbing constraints but I now need to recalculate
some results based on topologies with a ring-bound hydrogen mutating to a methyl
group. Is there an exact way to do this in gromacs using BAR?
More generally I'd be concerned about the accuracy of the linear extrapolation
of constraint dv/dl - depending on how you set out your transformation pathway I
would imagine you could end up skipping over a lot of detail in exactly this
kind of situation where a methyl group is 'pushing' out from a hydrogen.
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