Re: About heating...

From: David A. Case <>
Date: Wed 18 Dec 2002 11:42:51 -0800

On Wed, Dec 18, 2002, Andrei Leitão wrote:

> I am doing a molecular modeling study (500ps) to a DNA
> decamer including explicit solvent molecules (H2O) and
> counterions (Na+) at constant pressure.
> I made a molecular dynamic at 300K without this heating
> procedure and one of the end base pairs was very distorted
> from the axis.

Take a look at the equilibration procedure in the DNA tutorial on the
Amber web site. Two comments on your system:

(a) don't use constant pressure until the system is already heated up
at constant volume;

(b) generally, one should heat and equilibrate with constraints to the
initial structure (set ntr=1); after that is done, you can remove the

In spite of all of this, it is not unusual (or necessarily wrong) to see
an end base-pair distorted from the axis (although I don't know what you
really mean by "very distorted"...)

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Dec 18 2002 - 11:42:51 PST
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