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?
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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