[AMBER] Qns abt REMD simulations

From: Yew Mun Yip <yipy0005.gmail.com>
Date: Fri, 15 Nov 2013 18:51:49 +0800


I understand that there are 3 main components which make up a REMD simulation:

1) temp range
2) number of replicas
3) exchange probability/acceptance ratio.

Gromacs said that an exchange probability of 0.2 is usually a gd one. Is that true and are there any reviews/articles which gave this value as the recommended value as well.?

I also read that the first and second moments of the potential energy of the system can be used to determine the temp range. How do I find them using amber.?

Sorry for posting so many qns, but I hope to learn this well, so that I can be independent on running such simulations on my own asap. :)

With regards,
Yew Mun
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Received on Fri Nov 15 2013 - 03:00:02 PST
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