Re: Random Expulsion MD (REMD)

From: Vlad Cojocaru (
Date: Mon Oct 26 2009 - 06:45:30 CDT

Dear Kristian,

I don't know what do you mean by "Random Expulsion" but if you mean the
original method developed in Rebecca Wade's group (where I am working
now) I can provide you our newly developed tcl module to run this method
in NAMD.

This method has been originally published as "Random Expulsion Molecular
Dynamics (REMD)" but because of the abbreviation confusion with Replica
Exchange Molecular Dynamics (REMD), the method is now named "Random
Accelearation Molecular Dynamics" and was originally implemented in
AMBER8. We hope to post on our website the tcl module for NAMD soon.
Tests and documentation are almost completed. We also hope that in some
future release of NAMD, this module will be included. Until then, I can
send it to you in a private email.

However, I must say I am not sure this method is applicable to your
questions. We use this method to investigate pathways used by small
ligands to access buried active sites in proteins. This method was
neither intended nor used to investigate conformational changes in the
protein by applying the random forces on protein residues.
Maybe its another method you are looking for ...

Best wishes

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

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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