From: harish vashisth (
Date: Thu Jan 24 2008 - 12:25:20 CST

Hi Francesco,

    I have been working on something on similar lines...i have implemented
wade's algorithm in NAMD for my system...using SMD, it is not possible to
apply random forces but u can write a script of ur own using tcl-forces to
do that. i hope it helps.


On Jan 24, 2008 12:22 PM, Francesco Pietra <> wrote:

> As far as I can understand from descriptions (not having installed NAMD
> yet),
> Steered Molecular Dynamic (SMD) in NAMD is capable to apply an external
> force
> to a part of the system. Is that possible through SMD to apply a randomly
> generated force to the center of mass of a portion of the system, may be
> that a
> non-polymeric (drug-like) ligand of a protein to pull the ligand out and
> follow
> the path?
> Again, as far as I can understand from descriptions, that action should be
> possible with RAMD (Randomly Accelerated Molecular Dynamics) from Prof
> Wade
> group.
> Has anyone experience in comparing the two approaches?
> Thanks
> francesco pietra
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Harish Vashisth

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