Re: Accelerated MD in NAMD

From: Jeff Wereszczynski (
Date: Wed Nov 06 2013 - 12:00:29 CST

Hi James,

If you wanted to calculate the energy of just the dihedrals in just the
protein, you could specify an atom selection in the NAMDEnergy plugin to
VMD to analyze just that part of your system.

However, your boost energy is going to be applied to the entire system and
not just the protein, so the value you want to use is the total dihedral
energy for the system, which you already have calculated. Also, the
formula you quote is if you are applying a boost to all the energy terms in
the system. If you are just applying a boost to the dihedral terms, you
should use something more like this:


Thats just an initial guess, other people use different values. In your
case, the number_residues is the number of residues in your protein and in
your lipids. You can try those values and then if you are not getting
enough acceleration try adding the value of alpha you got to E.


Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology

On Wed, Nov 6, 2013 at 1:29 AM, James Starlight <>wrote:

> 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.
> so
> 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.
> James

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:57 CST