RE: Random Expulsion MD (REMD)

From: Brittany Morgan (brmorgan_at_clarku.edu)
Date: Mon Oct 26 2009 - 11:37:27 CDT

Dear Kristian,

A method called Rotamerically Induced Perturbation (boscoh.com/rip/) might
be adapted for your purposes. It was originally implemented in Amber, but it
works with NAMD as well (although that has not been extensively tested,
according to the website).

Brittany

kristian krantz wrote:
> Hi,
>
> Does anyone know of a way to apply forces randomly to the center of
> mass of one part of a protein to study conformational changes?
>
> Regards,
> Kristian

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