[gmx-users] REMD general protocol ...

[Justin Lemkul]

On 4/2/13 9:24 AM, rama david wrote:
> Thank you Massimo sandal, Justin and mark ,
>
> I also goes through the article and GMX archive.
> But I confuse with the protocol ( I am naive in REMD .
> So I want to conform protocol from the Expert and experience person )
>
> I will be grateful to you  for your suggestion.
>
>

The best training experience would be to take a simple example from the 
literature and reproduce it.  It is very hard to try to teach someone completely 
via email, especially since we do not know the scope and goals of what you are 
doing.

With respect to the question about pressure coupling stability over 310 - 360 K, 
I don't know offhand what to expect, but in general, I think this is a standard 
limitation within REMD and you'll probably encounter it.  Again, find a protocol 
for a similar system and try to get things working.  It will be easier to help 
you if you have a known objective that has been demonstrated to work.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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