Dear Amber users,
when running a npt dynamics with sander, one has to specify various
coupling parameters. In Amber 5 they are
tautp - time constant for heat bath coupling for the SOLUTE
tauts - the same for the SOLVENT
taup - pressure relaxation time
In A5 the default for tautp and tauts is 0.2 ps but the recommended value
FOR TAUTP is 0.5-5 ps - no hint for tauts. In A6 the default of tautp has
been changed to 1.0 ps while tauts seemingly doesn't exist as an input
parameter (at least I don't see it in the text manual on the web).
As for taup, the default of 0.2 ps and the recommended value of 1-5 ps are
both in A5 an A6.
This confuses me a bit. Can anybody comment on this? Which values would
you use? How sensitive is the choice? How does it influence the
simulations? And how is it with tauts in A6? Are
the values of tautp automatically used for the solvent as well? Does it
make a big difference if I use tauts = tautp = taup = 0.2 ps in A5? My
system is a 17bp DNA fragment with water and counterions.
Thank you for the answers.
Cheers,
Filip
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Dr. Filip Lankas
J.Heyrovsky Institute of Physical Chemistry
Czech Academy of Sciences
Dolejskova 3, 18200 Praha 8, Czech Republic
Phone +420-2-66053607 Fax +420-2-8582307
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Received on Wed Oct 03 2001 - 08:38:56 PDT
