AMBER Archive (2003)

Subject: Re: AMBER: NTX 5 or 7 after equilibration in constant pressure?

From: David A. Case (case_at_scripps.edu)
Date: Sat Aug 16 2003 - 19:04:18 CDT

On Sat, Aug 16, 2003, Majid moghaddam wrote:

> I am trying to do MD simulation on a peptide in
> water(TIP3P model). I did equilibration first in
> constant volume, then in constant pressure. now to
> start production run NTX must be 5 or 7?

For amber6, you need to set ntx=7 to force it to read the box size from
the input coordinates. This latter step is always done in amber7, so
either ntx=5 or 7 will work; (in amber7 the ntx=7 option is there only for
backwards compatiabilty with earlier scripts...ntx=5 and ntx=7 are actually
the same internally).

..good luck...dac 

-- 

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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.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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