Re: Accelerated MD in NAMD

From: James Starlight (
Date: Wed Nov 06 2013 - 12:50:36 CST

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?


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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