[gmx-users] REMD - low temperature ranges
kkuczera at ku.edu
Fri Apr 27 19:06:47 CEST 2012
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.
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
> 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:
> 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
> Of course, you could always read the reasoning provided by the
> authors in their paper, or email them for clarification...
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/ mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/
> <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
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/ Support/Mailing_Lists
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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users