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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 10 2007 - 06:07:53 PST
