Re: REST or RESTMD in NAMD?

From: francesco oteri (francesco.oteri_at_gmail.com)
Date: Tue Dec 11 2012 - 12:22:47 CST

Hi Gareth Shannon,
I am performing simulation with an evolution of REST (i.e. REST2, 1) using
gromacs.

It is interesting that in (2) a method using modified topologies for
running REST in gromacs has been developed.

This two information just to say that you can use the approach developed in
(2) to run (1) in NAMD.

Right now, I am smulating one protein (224 residues,3100 atoms) with 18340
TIP4P water molecules, 76460 atoms in total.
I need only 40replicas to have an everage acceptance ratio of 30%

1) http://dx.doi.org/10.1021/jp204407d
2) http://dx.doi.org/10.1002/jcc.21703

Francesco

2012/12/11 Gareth Shannon <paxgs1_at_nottingham.ac.uk>

> Hi all,****
>
> ** **
>
> May I ask if anyone has ever performed replica exchange with solute
> tempering (REST) (Pu Liu, Byungchan Kim, Richard A. Friesner, B. J.
> Berne. Proceedings of the National Academy of Sciences of the United States
> of America, Vol. 102, No. 39. (2005)) or replica exchange statistical
> temperature molecular dynamics (RESTMD)(Jaegil Kim, John E. Straub and Tom
> Keyes.* *The Journal of Physical Chemistry B. 116 (2012)) in NAMD?****
>
> ** **
>
> Many thanks,****
>
> ** **
>
> Gareth Shannon****
>
> ** **
>
> NASA Assistant Specialist****
>
> ** **
>
>
>
>

-- 
Cordiali saluti, Dr.Oteri Francesco

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