Hello all,
in the context of coarse-grained simulations in Amber, is there
any chance to use tabulated potentials/forces ? If not, are there some
plans
to include this possibility in future version/s ?
Let say just for non-bond ones (Vdw) (as regarding to
angle and torsion the actual harmonic form with properly mapped parameters
might be fully sufficient) ?
I guess that this feature is not available yet and only chance is here to
play with
LJ parameters introduced for the new coarse grained "atom types" using
proper
FRCMOD file. Am I right ?
But maybe should not be so difficult to implement tabulated non-bond
potentials
in actual Amber version just by rewriting LJ energy and LJ force functions
in that
way, that they accept relevant energy/force size tables (arrays) and
return proper values depending
on inter-particle distances and their difference vector (in case of
forces).
Also the function for reading the FRCMOD or simulation input files might
be probably customized a little
to put there some eventual information about the file/s from which the
proper energy/force values for each particle-particle
pair might be read.
Is this idea OK or I am too naive here and much easier would be to use for
this purpose
another softwares as DL-POLY, Espresso etc. ? If the above outlined idea
might be
implemented relatively easily, which are the concrete names of the
functions/files
to modify (e.g. LJ(VdW) energy/force function, function to read input
files ...)
Thanks a lot in advance for any suggestions here !
Best wishes,
Marek
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Received on Thu Feb 23 2012 - 09:30:02 PST
