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

Justin A. Lemkul jalemkul at vt.edu
Sat May 19 20:47:43 CEST 2012

On 5/19/12 1:13 PM, jrustad wrote:
> 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
> could:
> (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.

I don't know how complex the system is you're dealing with, but at this point, 
isn't it just far more straightforward to construct a rudimentary force field 
with a few atom types rather than rely on (slow) tabulated functions and 
potential funny business to get the free energy code to work?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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