Re: [AMBER] help in density equilibration

From: David A Case <>
Date: Mon, 24 Aug 2015 08:47:41 -0400

On Mon, Aug 24, 2015, Robin Jain wrote:

> I am equilibrating my system at NTP. Now i want to know two things-
> 1. on using CheckMD command i got following message-
> there is vacuum space in the box for .... 2.000A diameter spheres. what
> does it means

It means you have a "vacuum bubble" in your simulation, indicative of
insufficient equilibration. Does the message really say "....", or is
something else there? It's hard to say much, since we don't know anything
about your system, or about what sort of equilibration you have done.

> 2. how could i got desired experimental density under NPT condition.

You can't. The density that is achieved after NPT equilibration will be
what ever is preferred by the force field you choose. If you really want
to run a simulation at the experimental density (most people don't), then
you would need to set up a system with the proper volume, and use the NVT
model to keep the density fixed.


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Received on Mon Aug 24 2015 - 06:00:10 PDT
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