Re: colvar for PMF calculation

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Apr 21 2010 - 05:13:48 CDT

Hello Navendu,

Technically, the colvars in NAMD allow you to do this (using the
keyword outputAppliedForce). A warning, though: trying this using an
atomistic model would be much too complex and expensive to sample
properly. So my advice is to do it using a coarse-grained model (you
probably don't care about atomic detail anyway).

Best,
Jerome

On 21 April 2010 01:02, Navendu bhatnagar <navendu.bhatnagar_at_gmail.com> wrote:
>
> Hello,
>
> This mail is regarding the use of  COLVAR module for PMF calculations in
> NAMD
>
> I have performed protein-lipid interaction MD simulations using NAMD engine
> and as a part of analysis, I need to calculate the PMF
> of these interactions. The way this will be done  is by performing a set of
> calculations for varied distances
>  along a reaction coordinate which is a vector between the center of mass of
> protein and the bilayer in the 'z'-direction (normal to the bilayer surface)
>
> The bilayer and protein backbone shall be constrained using a spring
> constant and the restraint forces will be evaluated at every stage.
>
> My question here is that does SMD COLVAR method supports this kind of
> calculation ?
> The reason I ask is because I need a restraint force as output but I don't
> see that option in the COLVAR documentation in NAMD user guide.
>
> Thanks
>
> --
> NAVENDU BHATNAGAR
> Deptt. of Chemical Engineering
> WAYNE STATE UNIVERSITY
>

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