Hi,
> When I observed the dV/dL averages for 500ps for lambda = 0.99, the
> restraint energy is -177.4749 kcal/mol which is the almost all the dV/dL
> for my system.
> The reason I had the restraints was to make sure that the K+ and Cl- dont
> come close during the dual mutation.
>
> Is there a better way to approach this?
I am not sure what you ultimately want to do, so it is difficult to
distinguish better and worse ways to do it here. Decoupling a restrained
molecule from its surroundings is a different thing from decoupling a
non-restrained one, with resulting differences in free energy. Both ways
make sense in terms of different calculations.
If you want the two ions to be restrained in V0 only, then your setup is
good to go, but shows (unavoidable?) convergence problems at high lambdas.
If you want the restraints to not count for dvdl, set dvdl_norest, or
define the restraint as a distance between K and Cl instead of cartesian
ones. Or, remove the restraints altogether (which, indeed may also give
you poor sampling as K and Cl can stick together).
None of these things is wrong per se, they just answer different questions.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jan 19 2012 - 03:00:03 PST
