AMBER Archive (2003)

Subject: Re: AMBER: AMBER and NAMD

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Sun Jul 27 2003 - 11:10:10 CDT

On Sun, 27 Jul 2003, Vlad Cojocaru wrote:

> Dear Amber users,
> Has anyone try to run NAMD with AMBER input?
...Yes, me for example :-)
> If yes can somebody tell
> me what would be the equivalent of "ntt=1, tautp=2.0" in NAMD??
..The description of the temperature coupling in the NAMD manual
is quite terse. However, it refers to the X-PLOR manual for details (which
id freely available, I believe).
> Is tautp
> constant the coefficien that they are talking about in the tCoupleFile
> (namd user guide)?.
> Could namd do the same simulated annealing protocol as described at
> page 135 in amber manual?
...NAMD can only do 'vacuum' or 'explicit solvent' calculations.
The example on p. 135 uses 'eedmeth=5'. It would require some
manual intervention (=programming) to get namd to do 'epsilon=r'
electrostatics.
I'd suggest doing things like simulated annealing with AMBER (sander)
or NAB (which allows arbitrarily creative annealing protocols :-)
and then switching to NAMD for the solvated system. Search
 the AMBER mail reflector archive for Luis Gracia's message
on how to get rigid TIP3P waters in NAMD.
good luck
Andreas 

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