AMBER Archive (2002)

Subject: Re: problem in PME

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 12 2002 - 08:06:47 CST

On Tue, Nov 12, 2002, Monica wrote:

> I am running DRU-DNA complex on AMBER6 in vacuum....

> My input file is:
>
> B&cntrl
> imin=1, ncyc=50, maxcyc=1000, nmropt=1, cut=8.0,
> ntpr=100, ntb=1, scee=1.2, ntr=1, scee=1.2
> &end

Setting ntb=1 implies you have a periodic simulation, not a vacuum. My
recollection was that we also recommended using sander_classic for vacuum
calculations in Amber 6. You can get things to work in sander (check the
instructions or the mail archives carefully), but this was less efficient
than running the calculation with sander_classic.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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