AMBER Archive (2009)

Subject: RE: Re: [AMBER] box problem

From: Ross Walker (
Date: Sun Aug 16 2009 - 11:59:59 CDT

Hi Nancy,

Am I right in thinking here that what you mean is you do not want the entire
system solvated? I'm not sure why you would necessarily want this but if I
assume this is what you want to do then you will not be running periodic
boundary simulations I assume. Of course in this case your water will
immediately boil off into vacuum so you will need to use some kind of
solvent cap with a restraint on the edges of the cap. You can do this using
the solvatecap command in leap. You give it a radius for the water to be
added and also a center. By centering it on the end of your tube you should
be able to create a water distribution (albeit spherical) at the end of your
carbon nanotubes.

Good luck,

> -----Original Message-----
> From: [] On
> Behalf Of Nancy
> Sent: Thursday, August 13, 2009 7:43 PM
> To: AMBER Mailing List
> Subject: Re:Re: [AMBER] box problem
> Thank you case for your patience. I have four carbon nanotubes packed
> together. There is a layer of water in the nozzle. I want water flow
> through the tubes,not escape from the space between tubes and box,it is
> just like the how to add suitable box in xleap?
> Thanks in advance!
> ?

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