On 2010-12-24 13.15, ms wrote:
On 24/12/10 10:36, David van der Spoel wrote:
On 2010-12-24 11.04, Mark Abraham wrote:
On 22/12/2010 5:44 PM, Qin Qiao wrote:
Dear all,
I posted yesterday but didn't get answer..I guess it's due to my wrong
approach to ask. I would like to explain more and hope I would get
your help.
I'm doing an REMD, and want to have a strong temperature coupling to
make sure every replica is at its target temperature. I guess I could
do it by setting tau_t small in the Nose-hoover T coupling, but there
will come the warning in Gromacs.
I maxwarned the warning to proceed, and find the temperature is ok,
but I am not sure whether it will introduce some artifacts in the
simulation and what kind of artifacts. Could you tell me? Thanks a lot.
The temperature coupling algorithms are discussed in the literature,
when they were derived (citations in GROMACS manual) and subsequently. I
suggest you do your own homework there. The use of REMD is more or less
irrelevant to the trade-offs when deciding what temperature coupling
scheme to use.
That is correct, but do not use Berendsen! There is a recent paper from
the Garcia group (IIRC) about the effect of Berendsen coupling on REMD
sampling. Not good.
Mark
I'm not an expert, but isn't Berendsen usually not used because it
doesn't give a correct ensemble? I may be partial because I personally
know Giovanni Bussi, but it seems from what I've heard that v-rescale is
the best choice usually.
V-rescale is a good choice. Berendsen not only gives you the wrong
ensemble but it also biases the energy distribution to lower energies.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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