AMBER Archive (2002)

Subject: Re: water molecules diffuse during equilibration

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 16 2002 - 20:31:12 CDT

On Tue, Jul 16, 2002, Qing Zhang wrote:
>
> I saw water molecules diffused during const. P
> equilibration with PME, even periodic boundary was
> used. The Amber 6 manual says that's because PME does
> not image residues in the same manner as standard
> Amber, and the program ptraj can convert PME imaging
> to standard imaging. But I can not find this function
> from ptraj's manual. Does anyone know why?

ptraj commands are listed alphabetically in section 11.4 of the Amber 6
Users' Manual (section 8.4 in the Amber 7 manual).

In particular, the image command is described on p. 287 (Amber 6) or
p. 202 (Amber 7).

I'm sorry it was hard to find. In our defense, it *is* in bold-face
type, and the entire chapter is only 16 pages long....

..hope this helps...dac 

-- 

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