Re: SMD vs RAMD

From: harish vashisth (harish.vashisth_at_gmail.com)
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.

-harish

On Jan 24, 2008 12:22 PM, Francesco Pietra <chiendarret_at_yahoo.com> 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
>
>
>
> ____________________________________________________________________________________
> Looking for last minute shopping deals?
> Find them fast with Yahoo! Search.
> http://tools.search.yahoo.com/newsearch/category.php?category=shopping
>
>

-- 
Harish Vashisth

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:12 CST