[gmx-users] connecting two atoms with a user-defined potential

[Michael Brunsteiner]

--- Michael Shirts <mrshirts at stanford.edu> wrote:
> 
> Hi, all-
> 
> I'm interested in coupling atoms with user-defined flat-bottomed
> potential.
> I've been trying to figure out how I can set things up such that I
> can get
> two atoms to interact using the user-defined potentials, without
> kludging the
> code too much.  I noticed that one can load in a tablulated, but it
> doesn't
> appear clear how it can be applied to just _some_ pairs of atoms, not
> all pairs. 

Can't do this (AFAIK). Alternatively you can use the umbrella
sampling part of the pull code. This, however, only allows for
harmonic (as opposed to flat bottomed) potentials.
Though, it should be fairly easy to modify the code in
mdlib/pull.c to replace the harmonic by a flat bottomed potential.
(also have a look at the "external potentials" topic, as recently
discussed in the gmx-developers mailing list)

regards
michael

ps: out of couriosity, is this supposed to renstrain a ligand
in a binding pocket in a free energy calc as suggested by
by, e.g., Rebecca Wade ? If so, how do you plan to correct dA for the
restraint?


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