AMBER Archive (2003)

Subject: Re: minimization with fixed UC dimensions

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Feb 21 2003 - 19:24:32 CST

Thank you for your reply, the reason why I asked this is because for
example Cerius2 has such a feature (to vary or not the cell paramters
during minimization). It helps to reduce distortions if one starts with a
structure where there is a big stress buildup. For such a structure if one
does first minimize the atoms but not the unit cell and then minimize also
the UC parameters the UC is less distorted. It is just a more gentle way
of minimizing a system (especially systems that one builds by hand, when
no crystal structures are available or some good guess initial structure)

That's what I know from my experience at least.

Ioana

On Fri, 21 Feb 2003, David A. Case wrote:

> On Fri, Feb 21, 2003, Ioana Cozmuta wrote:
> >
> > Is there an option in amber to perform minimization keeping the UC
> > dimensions fixed and then release the angles and the lengths of the UC and
> > minimize again?
>
> There is no such option. It is not clear to me why one would want to do this.
> Minimization (at best) corresponds to a zero Kelvin model (but without any
> zero-point vibrations). You *can* optimize unit cell lengths (but currently
> not the angles) at finite temperatures by carrying out constant pressure MD
> simulations.
>
> ..hope this helps...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>