[gmx-users] Re: BAR calculations with tabulated non-bonded potentials

jrustad rustadjr at corning.com
Sat May 19 19:13:59 CEST 2012

Thanks- yes, I suspected this might be the case, however, in the context of a
free energy calculation it seems difficult to associate the lookup table
with a molecule type rather than an atom type.  In other words, I have
defined a molecule "Fe" which will change from Fe2 to Fe3.  

So, its true that the code seems to want a single lookup table to be
associated with the molecule from the beginning (rather than an atomtype),
which suggests that I can't do what I want to do in a straightforward way.

I thought of a possible fix last night- I could define two "molecules" Fe2
and Fe3, assign lookup tables using "energygrps" in the normal way.  Then I
(1) turn off the interaction between the two "molecules" 
(2) put in a constraint to force them to be on top of each other.  

Then I could fix things so that as lambda went from 0 1, the Fe2 turns on,
and the Fe3 shuts off.

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