[gmx-users] REMD general protocol ...
ramadavidgroup at gmail.com
Tue Apr 2 19:02:43 CEST 2013
Thank you justin.
I will do the same.
On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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