From: Andreas Svrcek-Seiler <>
Date: Sun, 27 Jul 2003 18:10:10 +0200 (CEST)

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'
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

           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
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Received on Sun Jul 27 2003 - 17:53:01 PDT
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