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
Best,
Qin
2010/12/21 Qin Qiao <[email protected] <mailto:[email protected]>>
Dear all,
I wonder what will happen in Nose-hoover coupling when tau_t = dt
* nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to
ignore the Gromacs warning)
I tried this setting, to 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 in advance.
Best,
Qin
--
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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