Re: Accelerated MD in NAMD

From: James Starlight (
Date: Wed Nov 06 2013 - 01:29:53 CST

I try to specify my question dealing with more specified case:

assuming I'm modelling activation of the membrane receptor (R->R*) which
involves motion of the part of its helix which are not in the membrane but
exposed to the solvent. So the energy for such conformation change
(assuming that amplitude of such displacement could be ~ 3-5 A) could be ~
several kT. Therefore in equilibrium aMD I've never seen such transition
due to big energy barrier between R and R*. Addition of the boost potential
to dihedral term might solve this kinetic problem.

1) firstly I need to compute the averaged Dihedral term for my protein only
along the trajectory
for the entire system with the VMD namdstats.tcl script (consisted of
lipids as well) I have DIHED: 10068.803885714286
How I could compute such value for only protein (excluding lipids)?

2) than assuming that E threshold = barrier height (several Kt) for the
receptor of 350 atoms I have

Eth= <Uav>+167 (according to the empirical formula U+1/3*number of atoms)
alpha= 280 (4/5* number of atoms) > but not sure in this value because I'd
like to preserve shape of the initial potential surface without its
modification (only decreasing barrier height for the most stable (R) state=
deeper potential well).
So addition of such boost should increase transition rates across barrier
in several times (I could not still understood the full meanings of the
coefficient in that formulas). Does this statements correct?

I'll be thankful for any suggestions.


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