SMD vs RAMD

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Jan 24 2008 - 11:22:18 CST

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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