Hi,
In general lowering the value of alpha is an easy way to increase the
boost when it's active. In my experience aMD requires a lot of
tinkering with before you get parameters that really work for you
(fortunately short MD runs are usually all that's needed to get an
idea for how a set of parameters will behave on average). Keep in mind
though that as you increase your boost you're going to be increasing
your statistical noise as well which is going to make reweighting the
data from the simulation more difficult.
-Dan
On Fri, Mar 27, 2015 at 9:39 AM, Brian Radak
<brian.radak.accts.gmail.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Mar 27 2015 - 09:00:04 PDT
