Re: SMD vs RAMD

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jan 24 2008 - 12:28:37 CST

Hi Francesco,

As I am working with RAMD, I might be able to answer your question. In
RAMD, a random force is added on the COM of the ligand for N MD steps.
After N steps, the movement of the ligand is assessed against a
user-defined threshold. if the distance d between the COM position
before and after the N steps is higher than the threshold, the same
force will be applied for the next N steps. However, if d is lower than
the threshold, the direction of the force will be changed. Therefore,
during a RAMD run you will have a lots of different force directions
generated before the ligand goes out. Therefore, you dont need to know a
priori the ligand release path. The method is useful for finding pathways

In SMD, the direction of the applied force is known a priori and the
ligand is pulled in that direction during the whole simulation. The
method is useful for getting the force profile for the ligand release
via the defined pathway (or the free energy profile if combined with
Jarzynski's equality). Details about SMD are very nicely covered in the
NAMD documentation (references to the original papers are also there).

If you have further question about the use of RAMD, please contact me.

Best
vlad

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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