AMBER Archive (2004)

Subject: Re: AMBER: about amber8, replica exchange

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri May 28 2004 - 22:55:34 CDT

see answers below

> Dear Amber users,
>
> I am very interested in the replica exchange MD in amber 8
> However, after reading the user guide, I can not find
> where I can change the exchange frequency between replicas,
> I mean after how many MD steps amber will exchange replicas.
>

nstlim sets the number of steps between exchange attempts, and numexch
is the number of exchange attempts.

> And another question:
> When determining whether the exchange occurs, the potential
> energy (E) of each replica must be known. Does amber use
> the AVERAGE energy during the short running or the energy
> of the last second? why?
>

it uses the instantaneous energy, since that is the energy
of the structures that are being considered for exchange.

> Thank you very much.
>
> Best Regards,
>
> ---
> J. Zhang, Dr
> Institute of Biophysics
> Nanjing University
>
>
>
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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