Dear Amberites,
I think many people have noticed that in sander of Amber 6 and 7, the NTT
options have been restricted to NTT=0, 1, and 4. This probably means now
AMBER doesn't encourage people to use independent thermostats for
couplings to solute and solvent. I can understand that multiple
thermostats are intuitively artificial, but I thought such an approach was
meant to remedy the problem of "hot solvent, cold solute" or
"inhomogeneous temperature gradient" artifacts. I know that a good source
of related discussions can be found in the article by Harvey et al. J.
Comp. Chem., 19, 726-740 (1998) "The Flying Ice Cube ....", but it is
still not clear to me if the problem with NTT=1 (single thermostat) can be
remedied by removing center of mass motions alone (probably with the
particle mesh Ewald method).
I have spent some time looking for recent articels that have readdressed
this issue, but I just haven't found good ones. Could anyone provide me
with the "insider information" for the reason why other NTT options have
been turned off, and whether the temperature inhomogenity problem is gone?
Any good references for addressing these questions are also more than
welcome.
Thank you in advances for the helps,
Jung-Hsin
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Jung-Hsin Lin, Dr. rer. nat.
Howard Hughes Medical Institute and
Department of Chemistry & Biochemistry TEL: +1 858 534 0956
University of California, San Diego FAX: +1 858 534 7042
9500 Gilman Drive, MC 0365 WWW: http://mccammon.ucsd.edu/~jlin/
La Jolla, CA 92093-0365 U.S.A.
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Received on Mon Apr 29 2002 - 16:10:30 PDT
