Hello,
I'm attempting to run an energy minimization on some high energy conformers
of a polymer dimer while restraining two dihedral angles pertaining to the
five backbone carbons of interest. The literature and forums online are
sparse when it comes to non-biochemical systems, and it seems as though the
syntax might have changed over the updated versions of GROMACS.
I've attempted to implement this bit in my topology:
#ifdef DIHRE
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
2 1 8 29 1 1 52 0 1 2
3 2 1 8 1 1 75 0 1 2
#endif
As well as this bit in my .mdp file:
define = -DDIHRE
; Dihedral Restraints
dihre = yes
dihre_fc = 1000
dihre_tau = 0.0
nstdihreout = 50
I've also tried using what I think is the more recent syntax for applying
restraints:
; position restraints for System of UNNAMED
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
8 1 1000 1000 1000
29 1 1000 1000 1000
However, when I energy minimize and read the backbone dihedral angles they
are different than the ones I started with! I am sure I have the correct
atom numbers (1,2,3,8,29), but am not sure why GROMACS is reading them and
then ignoring my restraints.
Any ideas?
Thank you very much,
Harrison
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