[gmx-users] regarding dihedral restraints
Sadaf Rani
sadafrani6 at gmail.com
Mon Mar 2 18:42:26 CET 2020
Dear Gromacs users
I am restraining three dihedral angles between atoms of two
different residues. when I measure it using the following command:-
gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of
trans.xvg
I am getting one of my dihedrals graphs as mentioned in the link.
https://www.dropbox.com/home/dihedral_angles
My dihedral angles have a multiplicity of 1 as mentioned below:-
[ dihedral_restraints ]
; ai aj ak al type phiA dphiA fcA phiB dphiB
fcB
72 74 31 33 1 146.72 0.0 0 146.72 0.0
41.840
75 74 31 27 1 173.10 0.0 0 173.10 0.0 41.840
75 74 31 25 1 158.21 0.0 0 158.21 0.0 41.840
However, in gromacs manual, I read this:-
*Counting transitions only works for dihedrals with multiplicity 3*
Am I doing something wrong? How should I measure dihedral restraint over
time?
Thanks.
Sadaf
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