[gmx-users] REMD - low temperature ranges

[Krzysztof Kuczera]

If you are only interested in conformational sampling, then it makes 
sense to start at 300 K or even higher - maybe 320 K. The main reason 
for working at lower temperatures is if your system
is unstable - eg. if you expect that the molecule will be mostly 
unfolded at 300 K and you want to sample the folded state. Another 
reason might be having experimental data at lower T, but this
is problematic, as it is hard to model temperature-dependent properties 
with simple force fields.

Krzysztof Kuczera

On 4/27/12 10:06 AM, Tomek Wlodarski wrote:
> Hi Mark,
>
> Thanks for reply.
>
> The problem is that I have never found in the papers reasoning behind 
> the the lower than 300K temperatures.
> Moreover, authors were interested in properties in 300K or above.
> I was wondering if this is not based on experience that REMD 
> implemented in gromacs works better when you also include lower 
> temperature.?
> best!
>
> tomek
>
> On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:
>
>         Hi,
>
>         I have notice that quite often people in REMD simulation use
>         replicas in lower than 300K temp.
>         Using for example temperature ranges from 250 to 450K
>         I am wondering what is the purpose of those replicas.
>         I have limited computational resources and I am wondering if
>         for studing 175 aa protein is better to start from 250K and up
>         to 350 K or choose from 300-400K (just an example)
>
>
>     Depends on the temperature(s) at which you wish to make
>     observations. Sampling is normally enhanced at higher
>     temperatures, so unless you want the ensemble at some low
>     temperatures, it is normal to start at your lowest observation
>     temperature.
>
>     Of course, you could always read the reasoning provided by the
>     authors in their paper, or email them for clarification...
>
>     Mark
>     -- 
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-- 
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html


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