this is a minimization of all coordinates with
respect to the total forces. this includes
bonds, angles, dihedrals, electrostatics, etc.
it also includes the restraint potential.
With decreasing force constants it becomes
easier to move away from the reference coordinates.
Carlos
----- Original Message -----
From: "A. Hungie" <hungie01.hotmail.com>
To: <amber.heimdal.compchem.ucsf.edu>
Sent: Tuesday, May 06, 2003 8:57 AM
Subject: minimization with restraints
> Dear All,
>
> I have a look in a DNA simulation tutorial in Amber homepage. In step 3
> (moving DNA), DNA was minimized 6 rounds by decreasing force constant from
> 25 to 0 kcal/(mol.A**2). As my understanding, this minimization is only
bond
> length minimization, right? Are bond angle and dihedral angle minimized?
> Thank you very much in advance for your kindness response.
>
> Hungie
>
>
>
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Received on Tue May 06 2003 - 14:53:01 PDT
