AMBER Archive (2006)

Subject: AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes

From: Michael Mazanetz (paxmm2_at_nottingham.ac.uk)
Date: Wed Sep 13 2006 - 15:42:02 CDT

Dear Amber Users,

I am running simulations where I'm varying the LJ potentials between specified (DM) residues. I'm doing this by altering the NONB parameter of the frcmod input files. This consequently changes the prmtop files generated in LEaP. Can someone explain how the values are generated in the prmtop examples below as a consequence of the changes I'm making in the frcmod files.
Many thanks in advance:
Mike

DUM1.frcmod
Parameter set for DM particles
MASS
DM 10.0

NONB
DM 1.4000 0.1000

1.prmtop
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  2.32218265E+04 1.26135508E+05 5.81935564E+05 0.00000000E+00 0.00000000E+00
  0.00000000E+00
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  9.63780608E+01 2.49407537E+02 5.94825035E+02 0.00000000E+00 0.00000000E+00
  0.00000000E+00

-------------------------------------------------------------------
DUM2.frcmod
Parameter set for DM particles
MASS
DM 10.0

NONB
DM 1.4000 0.0100

2.prmtop
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  2.32218265E+03 3.98875500E+04 5.81935564E+05 0.00000000E+00 0.00000000E+00
  0.00000000E+00
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  9.63780608E+00 7.88695883E+01 5.94825035E+02 0.00000000E+00 0.00000000E+00
  0.00000000E+00

-------------------------------------------------------------------
DUM3.frcmod
Parameter set for DM particles
MASS
DM 10.0

NONB
DM 1.4000 0.6000

3.prmtop
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  1.39330959E+05 3.08967634E+05 5.81935564E+05 0.00000000E+00 0.00000000E+00
  0.00000000E+00
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  5.78268365E+02 6.10921204E+02 5.94825035E+02 0.00000000E+00 0.00000000E+00
  0.00000000E+00

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