Does anyone have experience with or can recommend a boost selection
protocol for aMD with CHARMM36?
I am trying to get a phi/psi torsion PMF and acidic proton torsion PMF for
aspartate dipeptide (in explicit solvent). I borrowed what I thought were
fairly aggressive parameters from a paper using NAMD, in which the
following was recommended (using AMBER terminology here):
ethreshd = <U_dihedral> + cN
alphad = cN
where c = 0.5, N is the number of solute atoms, and <U_dihedral> is the
average dihedral energy (excluding 1-4 non-bonded terms I guess?).
I ran a short (100ps) simulation and got <U_dihedral> ~= 3.5 kcal/mol and
then calculated parameters as above. A fairly long (10ns) production run
then gave an average boost of 2.2 +/- 0.9. However this really only samples
the lowest energy phi/psi states and never flips the carboxylate proton at
all (a barrier of ~4 kcal/mol).
Any suggestions appreciated,
Brian
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Fri Mar 27 2015 - 09:00:02 PDT
