Dear Marek
We have a VERY preliminary version of pmemd that does what you mentioned.
It read tables for coarse grained potentials, but requires new
'atom/residue' definitions, etc.
It was a 2-3 months job to create a working version for the Hill/Voth
potentials.
We have that working now in a not very elegantly written version.
Please contact me off-line if you want to discuss this further.
Adrian
On 2/23/12 11:53 AM, Marek Maly wrote:
> 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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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Thu Feb 23 2012 - 09:30:03 PST
