[gmx-users] bond angles and (improper) dihedrals angles in PRODRG
hugo at acd.ufrj.br
Tue Aug 13 16:13:25 CEST 2002
Hi to all,
in the PRODRG paper (J.Comp.Aid.Mol.Des., 1996, 10, 255-262) it is shown that
bond, angle, improper dihedral angle and dihedral angle for a given molecule are
defined based on a GROMOS forcefield list containing information about optimal
distances, optimal angles and force constants. Were the terms on this parameter
list modified in GROMACS forcefield? How can I obtain this list?
Further in the same paper, it is told that if does not exist a previous
information about a certain combination of atoms in a bond or angle, the nearest
plausible code is selected, and the user will be warned if such case occur.
This warning is implemented in PRODRG Server?
I apologize if I missed something in the manual, the paper and/or the algorithm.
But I became curious about some c1 values (improper dihedrals) in .top file (I
think that it is a constant k in equation 4.51, pag. 57, of GROMCAS manual, it
is right?), 1673.6 and 836.8, one the half of the other.
Thanks is advance for any coment,
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