Re: AMBER: vdw energy in minimization

From: carlos <>
Date: Mon, 19 Jul 2004 08:13:30 -0400

please include the output for the MD part, it looks like your MD input
might not be right at the part the specifies the restraints (or it could
just be formatting change when you pasted into the mail).

A rise in vdw energy is not uncommon for a TIP3P solvated system, the
vdw energy of the water can be very high and is compensated by
large negative electrostatics.

Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:


> imin=1,
> maxcyc=15000, ncyc=4000, drms=0.001,
> ntb=1, ntr=1,
> cut=10,
> ntpr=50,
> &end Input for restraints (1-12) 10 RES 1 12 END
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Received on Mon Jul 19 2004 - 13:53:01 PDT
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