AMBER: Calculating dipole moments

From: Austin B. Yongye <>
Date: Wed, 28 Nov 2007 14:33:41 -0500 (EST)

Dear amber users,
I would like to calculate the dipole moments of a trisaccharide in
explicit water during the first equilibration stage of a thermodynamic
integration calculation.

When I use this input:
  Ligand_cap_coul trisaccharide
   nstlim=20000, nscm=2000,
   ntx=5, irest=1, ntb=2, ntpr=100, tempi=300.0, ig=974651,
   ntp=1, taup=1.0,
   dt=0.0001, nrespa=1,
   ntt=1, temp0=300.0, tautp=2.0,
   ntc=2, ntf=2, tol=0.000001,
   ntwr=10000, ntwx=100,
   scnb=1.0, scee=1.0, dielc=1, cut=10.0,
RES 1 4

The computed dipole moment is 122 +/- 32D.

However, when I use this other input for a single gas-phase structure,

Minimization everything
    imin=0, dielc=1,ntb=0,
    scee=1.0, scnb=1.0, cut=12.0,
RES 1 4

The dipole moment is 5.5D, which makes sense when compared with the
HF/6-31G* and B3LYP/6-31++G(2d,2p) values of 4.8D and 4.1D, respectively.

Please does anyone have any suggestions as to why the dipole moment from
the TI calculation is inconsistent with the QM values?

Austin B. Yongye
Complex Carbohydrate Research Center,
University of Georgia,
315 Riverbend Road,
Athens, GA 30602.
Phone: 706 542 0263

"...then, we learn better in a free spirit of curiosity, than under fear
and compulsion..." -St. Augustine of Hippo
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Received on Sun Dec 02 2007 - 06:07:11 PST
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