AMBER Archive (2000)

Subject: Re: OWFEG and other AMBER 6.0 manual issues

From: David Case (case_at_scripps.edu)
Date: Fri Feb 11 2000 - 11:54:44 CST


On Fri, Feb 11, 2000, CRAIG ANTHONY MARHEF wrote:
>
> The AMBER 6.0 manual for sander_classic says that the OWFEG method has been
> implemented yet there is no section in the manual describing it's use.
> Is OWFEG not implemented as of yet or is this an oversight in the
> documentation?

It is implemented (see the lg*.f files), but not yet documented. We are
aware of this, but don't have any real time scale for remedying it.

>
> Is NSNB still an option in the 6.0 version of sander?

Only in a "deprecated mode": see the discussion of NBFLAG on p. 147. In
general, users should not need to set nsnb any more: list updates are
generated automatically as needed.

>
> I assume that sander 6.0 does not include separate solute solvent temperature
> coupling as in sander_classic. Is this true? If so then tautp is for the
> system and not only the "SOLUTE" correct?

Right: The discussion of TAUTP on p. 141 should begin "Time constant for
heat bath coupling for the system."

Thanks for your input!

...dave case

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | WWW: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================