[gmx-users] REMD general protocol ...

[rama david]

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
>
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>