Re: AMBER: replicas trapped in a few low temperatures

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 10 Jul 2008 06:59:03 -0400

have you compared the overlap of potential energy distributions for
the temperatures? perhaps your spacing is not correct and the energy gap
is too large for successful exchange.

2008/7/10 Ye Mei <ymei.itcc.nju.edu.cn>:
> Dear Amber usersúČ
>
> I am working on the folding of a small peptide using REMD in Amber 10. Sometimes, a replica finds a low energy conformation, then it is annealed to the lowest temperature. After that, this replica seems to be trapped in a few, maybe two or three, low temperatures, with a high "back exchange" frequency.
> It there any suggestions that can make this replica sample more wide temperature space?
>
> Best regards,
>
> Ye Mei
> ymei.itcc.nju.edu.cn
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry of MOE
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2008-07-10
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>



-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo.scripps.edu
Received on Sun Jul 13 2008 - 06:07:25 PDT
Custom Search