From: Jeremy Parlin (jeremyparlin_at_gmail.com)
Date: Mon Apr 23 2012 - 16:38:31 CDT
I have a system with an ion bound in a protein pocket, with one distance
restraint on it set via colvars. I am trying to perform an FEP simulation,
where that ion changes species, while the colvar restraint stays applied.
I've set this system up, with both ions present in the topology file,
having the same initial coordinates, with the old ion set to annihilate and
the new one to exnihilate. This executes successfully, however, in the
early stages of the simulation, the new ion swims out of the pocket, since
it experiences no protein interactions holding it there. To remedy this,
I've tried to 'tie together' the two ions. I've tried to do this either
with a colvar distance constraint between the two ions (restraining the
distance to zero), or by creating a virtual bond in the PSF file (adding a
corresponding term to the parameter file). In either case, the simulation
fails on the very first step, with both ions having infinite velocity.
Thoughts on how to do this successfully? I'd really like to the exnihilated
and annihilated ions to be in effectively the same position as one another
at all times, but both to be allowed to fluctuate together within the
binding pocket subject to my colvar restraint.
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