AMBER Archive (2003)

Subject: Re: AMBER: AMBER and NAMD

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Sun Jul 27 2003 - 12:45:40 CDT

Thanks a lot for the Reply,
  I have two more questions:
1. If I heat the system in NAMD with the temperature reassignments
method (and not use the coupling scheme) ...would that make a much
difference comparing to AMBER simulations?
2. Is the simulation in NAMD altered if I already started it without
the trick to get rigid waters?
Thanks again,
Vlad

Andreas Svrcek-Seiler wrote:

>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
>
>
>
> 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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