[gmx-users] REMD vs MD

[hanna pdb]

Hi, 
well I guess it depends on what models you mean...
REMD is a technique to enhance the conformational sampling. So if you have a e.g. a protein that is disordered or has large 
disordered parts. Using REMD several copies of the same system are simulated, each replica at a 
different temperature. Then, each replica can explore a different portion of the conformational space: the higher temperature replicas are able to move between different regions of the potential energy surface without staying in any of them, while the lowest temperature replicas can get trapped in local minima and are able to accurately explore the regions of the potential energy surface. This way you can obtain more information about conformational space then by simple MD.

This paper might help: Y. Sugita, Y. Okamoto, Chem. Phys. Let., 314, 261 (1999)

best

> Date: Thu, 5 Sep 2013 11:34:47 +0800
> From: pqah123 at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] REMD vs MD
> 
> Hi all,
> 
> I just want to ask you which is about REMD..I just understanding about
> the MD simulation which is the basic one..If i have a several models
> that i need to see the interaction between them is it okay to use
> MD?Or i need to use REMD instead?
> 
> Thanks in advance,
> 
> -- 
> Best Regards,
> 
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> alternative email : syafiqahabdulghani at gmail.com @ GS33669 at mutiara.upm.edu.my
> -- 
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