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
--
========================================
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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