Re: Accelerated MD in NAMD

From: Thomas Evangelidis (
Date: Wed Nov 06 2013 - 15:21:52 CST


1) Be cautious about the boost you apply, lipid bilayers are labile
systems. Have a look at this paper for possible caveats and the effect of
different threshold and alpha values:

As the authors state at the end, selective aMD is ideal for
protein-membrane systems, however, it is not supported by NAMD. It will be
though available in the next AMBER release.


A bit off-topic question: is it possible to calculate frequencies of
properties like H-bonds from aMD trajectories by means of a reweighting

On 6 November 2013 23:03, Jeff Wereszczynski <> wrote:

> 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.
> Cheers,
> 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

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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