Re: AMBER: density equilibrium & harmonic restrain

From: David Case <>
Date: Thu, 2 Oct 2003 04:39:05 -0700

On Tue, Sep 30, 2003, yuann wrote:

> I tried to equilibrate my DNA-protein complex in TIP3P solvent...
> However, the solvent density just raises to about 0.85 after 40ps NPT
> ensemble, but it raises to about 1.05 while decreasing the harmonic
> force constant to a smaller value, like 0.2.

> This is my input for 40ps NPT ensemble:
> ntp=1, taup=0.02,

You should never use such a small value for taup. I would recommend some
much larger value, say 2-5 ps. I'm not sure what will happen as you are
allowing the volume of the system to change exceedingly quickly.

It is also possible that your results are related to the harmonic
constraint, but this seems less likely to me.

....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
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Oct 02 2003 - 12:53:01 PDT
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