Re: direction of pull in namd

From: Leandro Martínez (
Date: Tue Jan 29 2013 - 08:09:01 CST

Dear Raghav,

We have published a paper describing SMD simulations with varying pulling
direction some time ago:

 L. Martínez, I. Polikarpov, M. S. Skaf, * Only Subtle Protein
Conformational Adaptations Are Required for Ligand Binding to Thyroid
Hormone Receptors: Simulations Using a Novel Multipoint Steered Molecular
Dynamics Approach,* J. Phys. Chem. B, 112, 10741, 2008.
The technique is simple. Its details and its merits are described in the
paper. Unfortunately, I've lost the implementation of this method because
of a computer hardware failure (always backup...). It is not hard to
implement using the tclForces interface in namd, on the other hand. If
eventually code that again, I will let you know.


On Tue, Jan 29, 2013 at 11:18 AM, raghav singh <>wrote:

> Hello All,
> I am doing some single molecule pulling experiments and i wanted to know
> how to change the direction of pull in namd??
> by default it is determined by the vector connecting fixed and smd atoms
> in namd.
> if anyone has successfully implemented the changed in pulling direction in
> smd (namd)....please help me out here.
> Thank you
> regards
> Raghav

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