AMBER Archive (2007)

Subject: Re: AMBER: Hydrogen in a phosphate ion

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 09 2007 - 13:46:43 CST

On Fri, Jan 05, 2007, Nitin Bhardwaj wrote:

> I have been trying to simulate a molecule that has a hydrogen in a
> phosphate ion.

...

> But still the things are not working out, although H1 does not overlap with
> O2 anymore. There is only a single molecule containing the phosphate ion in
> a water box and as soon as the simulation starts the molecule moves out of
> the waterbox and waterbox gets divided into four boxes with a gap between
> these boxes.

This sounds like an imaging problem, and/or the result of an incomplete
equilibration. Be sure to use the image command in ptraj before visualizing
your trajectory. The gaps between boxes (if they are what I suspect they
are), should disappear after constant pressure equilibration.

For more help, you will need to post details about how you prepared and
equilibrated your water/phosphate system.

...good luck...dac

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