Re: How I can to change the force field function in NAMD for protein phi-value analysis

From: Giacomo Fiorin (
Date: Mon Oct 07 2013 - 08:30:34 CDT

Hello Juan, is there a chance that the phi-value (number of contacts within
a given cutoff) can be expressed as a *coordNum* collective variable? In
that case, a simple harmonic potential applied to it would do the trick.


On Mon, Oct 7, 2013 at 5:55 AM, Juan José Galano Frutos

> Hi dear all:
> I would like to perform MD simulations to one protein which we already
> have evaluated a series of kinetic and thermodynamic phi-values for a
> detailed conformational folding/unfolding analysis (transition and
> intermediate states included). In this sense, the literature suggest add a
> biasing energy term leading the system to increasingly close conformations
> to those suggested for the phi-values previously calculated.
> Such biasing pseudoenergy term is definde as (an step function):
> W(rho ,t)={[alpha * M(rho-rho0)˛]/2 if rho(t)> 0 , or 0 if rho (t)<0} (Paci E, Vendruscolo M, Dobson CM, Karplus M (2002) Determination of
> a transition state at atomic resolution from protein engineering data. J
> Mol Biol 324:151–163)
> where the parameter alpha controls the relative weight of the restraint
> term with respect to the force field, and rho0 is equal to the lowest value
> of the reaction coordinate reached by the system up to time t in the
> simulation.
> The reaction coordinate for the process, rho(t), is defined as the mean
> square difference between the phi-value(sim) and the experimentally
> determined phi-value(exp) values:
> rho(t)= 1/N * sum[phi-value(sim) - phi-value(exp)˛] from 1 to N,
> where N is the number of phi-value(exp) values used in the calculations.
> Meanwhile, phi-value(sim) for one conformation C in the simulation is
> defined as:
> phi-value(sim) = ni(C)/ni(native), where ni(C) is defined as the number
> of side-chain heavy atoms within a given cutoff distance. The ni(native)
> term is the same but for the native conformation.
> As you can see, I have clear what I would to do but I do not know is how
> in NAMD. I have some programming skills and I made some scripts but I'm not
> an expert in programming. I also researched and apparently this issue has
> explicitly not been implemented yet in NAMD. If someone could suggest me
> how to do it I would be happy.
> Thanks very much in advance.
> Juan José
> Ph. D Student
> Institute for Biocomputation and
> Complex Systems Physics (BIFI)
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Sciences Faculty,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza
> Spain
> TEL: +34 976 76 28 06

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