[gmx-users] doubt in remd

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 9 15:20:47 CEST 2013

On Tue, Apr 9, 2013 at 8:29 AM, Shine A <shine.a at iisertvm.ac.in> wrote:
> Respected sir,
>                     I successfully  completed REMD simulation. Now I am
> struggling with analysis part. Here how I select the global minimum  from
> replica? Can you give some suggestions about the analysis part?

Doing a simulation is useless until you have thought about what you
want to observe from it. Only then can you design the simulation so it
might show what you want to observe - or go do something more
profitable if it won't be possible to observe!

Constructing a free energy surface from the structures in a single
ensemble is straightforward (e.g. Baumketner & Shea papers), and that
the simulation was REMD is immaterial.


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