Re: [AMBER] ionic liquid simulation

From: David A Case <>
Date: Sun, 12 Jan 2014 13:57:50 -0500

On Sun, Jan 12, 2014, Saeed Nasiri wrote:

> I have a question about the ionic liquid simulation tutorial. why in this
> tutorial there aren't any step for equilibration of density heat or
> pressure (like the other tutorials)?

The MD simulation is at constant temperature and pressure. For analysis,
you would discard some initial part until the system is at a stable density
and energy. (This is an "advanced" tutorial, and assumes some familiarity
with running simulations and checking for equilibration.)


> another question about the sander and pmemd command, what is the difference
> between them? Is it possible to use pmemd instead of sander in the ionic
> liquid tutorial?

Yes...for this tutorial, one would probably want to use pmemd, since it is
faster. You can check this yourself (for timings). In general, if you
request some functionality that is not supported in pmemd, a pmemd run
will quit immediately, and tell you what the problem is.


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Received on Sun Jan 12 2014 - 11:00:03 PST
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