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

From: Carlos Simmerling <>
Date: Wed, 7 Nov 2018 14:37:29 -0500

Hi Zhonghua, just to add to the good info that Vinicius sent, I would be
concerned about running T-REMD on a protein of 88 amino acids. If you want
to keep the protein folded this might work (if you restrain most of it),
but without some sort of restraints it may unfold at higher temperature. I
am not aware of any applications of T-REMD on protein folding for a protein
of this size in explicit water, at least not using normal processors. You
may need to explore other methods to get the information that you need.
People here might be able to help if you can share a little more about what
you want to do.

On Wed, Nov 7, 2018 at 10:50 AM Cruzeiro,Vinicius Wilian D <> wrote:

> 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 <>
> 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 - 12:00:01 PST
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