On 2012-01-26 06:37, Gianluca Interlandi wrote:
Hi Mark,
Thanks for the answer. Just to be clear: you think that a too short
interval might introduce artefacts? I agree with this. So, do you think
that an interval between 1 and 10 ps could be a good value?
It also depends whether or not you use constant pressure, in which case
it makes sense to increase the time to long enough to let the volume relax.
I still do not understand why people do NVT REMD, because it makes all
but one replica have a pressure that is not the ambient pressure.
Gianluca
On Thu, 26 Jan 2012, Mark Abraham wrote:
On 26/01/2012 11:38 AM, Gianluca Interlandi wrote:
Hi,
I have been going through the How-to for REMD in gromacs:
http://www.gromacs.org/Documentation/How-tos/REMD
Is there a recommended value for the exchange interval and does it
depend on system size? For example, is an interval of 100 ps
appropriate for a sytem with 60,000 atoms? Is a too long interval
simply a waste of time or can it actually introduce artefacts?
There's literature by Sindhikara (sp?) and Roitberg that says you
should have a short an interval as possible, and other literature that
says you shouldn't go shorter than around the autocorrelation time of
PE, ~1ps. I don't buy the former, and think some of their data support
the latter, and have some of my own not-ready-for-publication data
that I think suggests artefacts from the former. Work from Hansmann et
al suggests that achieving steady-state replica flow is rather tricky
even for seemingly trivial peptides, so increasing the number of
exchange attempts might help a little. I'm not aware of any good case
for a long interval between attempts.
Mark
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Gianluca Interlandi, PhD [email protected]
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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