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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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