Darrell Koskinen wrote:
Dear GROMACS Gurus,
I assigned improper dihedrals to my graphene structuure but still see it
vibrating. Is this to be expected? I thought the purpose of improper
dihedrals was to keep planar structures planar.
There is still a force constant associated with the improper, so deviations from
absolute planarity are possible. Vibrations aren't unexpected, but any severe
distortions would be problematic.
-Justin
Here is a copy of a couple of sections of my topology file after
assigning the improper dihedrals to my graphene structure:
#define improper_dihedral improper_Z_CA_X_Y
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
3 1 2 5 1 improper_dihedral
2 1 3 7 1 improper_dihedral
2 1 4 9 1 improper_dihedral
1 2 5 11 1 improper_dihedral
1 2 6 13 1 improper_dihedral
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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