AMBER Archive (2008)

Subject: Re: AMBER: is in vacuo simulation neccessary?

From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Mon May 26 2008 - 00:44:20 CDT

Anamika Awasthi wrote:
>
>
> Dear Friends,
> Is this essential that we should do in vacuo simulation
> before molecular dynamics ina water box?

No.

> What is the significance of this? in some particular
> situation (if protein is very big) can we skip this?

A simulation step in vacuo can sometimes help relax starting structures
close enough to something physically reasonable that the simulation no
longer numerically explodes when you solvate and add heat. However a
vacuum EM stage would normally be just as effective at this. Analysis of
the actual vacuum trajectory would often serve no purpose at all, even
if the force field was parameterised for vacuum simulations.

Mark
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