Re: Accelerated MD in NAMD

From: Jeff Wereszczynski (
Date: Wed Nov 06 2013 - 15:03:00 CST

Hi James,

1. I would agree that using dual boost is typically the best bet. As you
say, the general idea is that the torsional boost will increasing the
sampling of your biomolecule, while the total boost term will likely help
with diffusive properties.

2. Your values sound reasonable to me, if you have an average total energy
of -360,000 kcal/mol and 100k atoms then values of E=-340,000k and
alpha=20k might be a good place to start. If you want to increase sampling
I would try increasing E (for example, E=-320,000) or decreasing alpha.

There have been a couple papers that have come out in the last year or so
looking at GPCR systems with aMD, I'm sure those will have more details and
you may find them interesting.


Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology

On Wed, Nov 6, 2013 at 12:50 PM, James Starlight <>wrote:

> Professor Wereszczynski,
> thank you for the explanations. Some of my suggestions:
> 1) Currently I'm interesting in the application of double boost to my
> protein-membrane system. As I understood the addition of the dihedrall
> bost can increase sampling mainly due to the increasing of the rotation
> (Sampling between +-60, 0 and 120 degrees states) in the phi and psi angles
> of polypeptide backbone as well as lipid tales (structural term). In
> addition the second (total boost, which depends on the <Utot> and the
> number of atoms) can increase sampling rate due to modifying diffusion
> rates of the solute into solvent. I suppose that for membrane-containing
> systems this could be especially significant because viscous lipids can
> significantly slave conformational dynamics of the protein increasing
> barriers between its different states.
> 2) Assuming <Utotal> ~ -360.000 (the most negative term is from the
> electrostatics) kcal/mol and the number of atoms is 100000 in my system I
> have obtained -340.000 Boost threshold as well as impirical value for
> alpha 20000 (100000/5). Than if I;d like to increase sampling I should a)
> decrease threshold and/or b) decrease alpha
> Does this statements correct?
> James
> 2013/11/6 Jeff Wereszczynski <>
>> 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:
>> E=<U_dihed>+4*number_residues
>> alpha=4/5*number_residues
>> 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.
>> Cheers,
>> 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

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