AMBER Archive (2008)

Subject: AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange

From: xiaonan zhang (heptoking_at_gmail.com)
Date: Wed Aug 20 2008 - 02:25:43 CDT

Dear Amber users:
       After reading relevant papers and the AMBER 9 manual chapters on LES
and REMD, I have a few
questions on the implementation of these kind of MD.

   1. It seems to me tha LES method is relatively computationally cheaper
   than REMD, since the latter usually requires square(Number of atoms)
   independent replicas at different temperatures.When the loop regions is
   bigger, that require quite a lot of replicas Is that right? Another question
   pertaining to parallel computation of REMD is: if a REMD require N replicas,
   does this mean at least N cpu should be used simultaneously??
   2. As Dr. Simmerling has noted in
>
> Generation of accurate protein loop conformations through low-barrier
> molecular dynamics. Proteins. 2003 Jun 1;51(4) 577-90.
>
   A soft-core potential energy was used. However, I did not find
   documentation on this in the AMBER 9 manual. Does this option exist in this
   distribution?
   3. As a non-expert in Molecular dynamics, I am pretty confused with the
   LES and REMD and various hybrid methods. If my goal is to refine the loop
   structure of a homology model, which method is better to obtain a reasonable
   loop folding with a reasonable computation effort? It seems to me that LES
   is better since the convergent behavior of the copies will usually suggest a
   reasonable fold.
   4. As there is no LES tutorial in the AMBER site and documentation is
   limited, It is a little bit difficult for me to grasp the LES method.
   Moreover, the Moil-view webpage:
   http://morita.chem.sunysb.edu/~carlos/moil-view.html is not reachable
   right now. More comprehensive documentation or guidance is needed. Are there
   any plans on this?

Thank you for your attention.
 Xiaonan Zhang
Shanghai public health clinical center

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