Re: [AMBER-Developers] ntb vs ifbox?

From: Yong Duan <duan.ucdavis.edu>
Date: Tue, 06 Dec 2011 14:17:11 -0800

Very good example, indeed!

However, as far as I know, you can not simply change ntb from 0 to 1 to
realize this. You need box information that requires editing prmtop and/or
restrt.

--
Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
530-754-7632
>
>Pedagogical example:
>
>"Here's a water droplet containing a protein.  Let's simulate that water
>droplet in a vacuum (or in the gas phase), and see what happens.  Water
>droplets leave via an evaporative process.  So we will impose PBCs to
>simulate the bulk solution phase (change ntb to 1), now what happens?"
> That is, IMO, a useful pedagogical tool that would require users to set
>ntb=0 for a periodic system, and not a situation in which you would want
>prmtop hacking to be the appropriate course of action.  (Just an example
>off the top of my head)
>
>-- 
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
>_______________________________________________
>AMBER-Developers mailing list
>AMBER-Developers.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers

Received on Tue Dec 06 2011 - 14:30:03 PST