Re: AMBER: Once again, "distance" command in ptraj

From: Thomas Cheatham <>
Date: Mon, 4 Jun 2007 22:22:45 -0600 (Mountain Daylight Time)

> trajin ../prod.mdcrd
> center :391 origin
> image origin center
> strip :WAT,OCT
> distance dist :60,157,254,351.CZ,CG,CD*,CE* :391 dist.list

I'm traveling so have sporatic e-mail, but my guess is that the "strip"
command is somehow invalidating the box information. Try moving the strip
to after the distance measurement... In the meantime, I'll track it down.

Also, Prof. Simmerling is partially correct; by default, if box
information is present, the distance command calculates the minimum imaged
distance regardless of your center/image specifications (unless you
specify the "noimage" keyword). The intent is/was to show the shortest
distance in periodic space. I think that somehow the "strip" is disabling
this, assuming you are correct that the trajectory has box information and
the prmtop had it and/or you specified it with the "box"
command..... likely it is a bug or feature, but I agree that the strip
should not automagically lead to ignoring the box info.

[If I do not respond back soon; e-mail me privately and I'll try to

-- tec3

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Received on Wed Jun 06 2007 - 06:07:25 PDT
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