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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
