Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors

From: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
Date: Wed, 7 Nov 2018 15:50:20 +0000

Hello Zhonghua,


The number of replicas required to cover well a given temperature range increases with the square root of the total number of degrees of freedom in the system (see Annual Reports in Computational Chemistry, Volume 2; 2006; pp 83–95 or Phys. Chem. Chem. Phys. 2008, 10 (15), 2073). An option that you have to significantly decrease the number of degrees of freedom is to perform implicit solvent simulations.


I hope this helps,


Vinícius Wilian D. Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

________________________________
From: Zhonghua Xia <zhonghua.xia.helmholtz-muenchen.de>
Sent: Wednesday, November 7, 2018 10:22:51 AM
To: AMBER Mailing List
Subject: [AMBER] REMD: What can I do with much larger replicas than the number of processors

Dear all,

I want to do T-REMD on my protein (88 AA, 1438 atoms) with TIP3P water box (5938 water molecules), as well as a counterion Cl-. I learn from the tutorial that the number of replicas should be equal to the square root of the total number of atoms. In my case, about 120 replicas…

Any help appreciated! My purpose is certainly to enhance sampling.

Kind regards,
Zhonghua
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Received on Wed Nov 07 2018 - 08:00:02 PST
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