From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Tue Jan 29 2013 - 10:46:15 CST
I found one of my implementations of this method. Actually it is not the
one used in that paper (it is more general in the sense that different
trajectories can be induced to different atoms at the same time, but you
need a trajectory file for each atom, defining approximately where the
atoms must go throughout the simulation).
I've just written detailed commentaries at the script which describe
precisely how it must be used. You can download it from here:
It is the "pathdriven-tclForces.tcl" script.
I hope it helps.
On Tue, Jan 29, 2013 at 12:09 PM, Leandro Martínez <
> 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 <raghavbioinfo_at_gmail.com>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
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