Re: AMBER: in vacuo parameters

From: Carlos Simmerling <>
Date: Tue, 15 Mar 2005 18:29:31 -0500

from a physical standpoint, what do you mean by in vacuo
periodicity? Whether it is periodic or not doesn't really depend
on what you solvent is- in vacuo means that your solute is
surrounded by "nothing", so no other molecules need to be
included. Condensed phases usually work better with perdiodicity to
handle the edge of your system where it can't just turn
into empty space.

I think the manual means to disable periodicity when you don't want it.
If your case is a condensed phase, then use it.

Stern, Julie wrote:

>Hello Amber-ites,
> The AMBER 8 tutorial says that for in-vacuo simulations, periodicity
>needs to be disabled. Is this true and can you explain why? The problem
>that I'm working on involves alkane chains which are supposed to move so I
>need the periodicity in-vacuo. Are there any ways around this constraint?
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Received on Tue Mar 15 2005 - 23:53:00 PST
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