GROMACS version: 2022
GROMACS modification: No
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I have first carried out enforced rotation of single gamma subunit of ATP synthese with the following mpd parameters:
md.mdp (3.5 KB)
; Enforced rotation parameters
rotation = yes ; apply rotation potential (yes/no)
rot-nstrout = 1 ; output frequency (in steps) for the angle of the rotation group, as well as for the torque and the rotation potential energy
rot-nstsout = 10 ; output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers
rot-ngroups = 1 ; number of rotation groups
rot-group0 = CA_&_a_1-4760 ; name of rotation group 0 in the index file " index.ndx"
rot-type0 = flex2 ;
rot-massw0 = no ; use mass weighted rotation group positions
rot-vec0 = 0 0 1 ; rotation vector, will get normalised
rot-rate0 = 0.21 ; reference rotation rate (degree/ps) for group 0
rot-k0 = 600 ; force constance (kJ/(mol*nm^2)) for group 0
rot-fit-method0 = rmsd ; fetting method to determine angle of rotation group (rmsd, norm, or potential)
rot-eps0 = 0.0001
rot-min-gauss0 =0.001
rot-slab-dist0 =1
The simulation was performed in vflex2 mode with rot_vec in z direction. The simulation ran successfully with the single gamma protein.
However, when we tried to replicate the enforced rotation (with same mdp parameters) in six hexamer of alpha and beta subunits, the simulation was indeed ran without any error. However, we didn;t observe any rotaion in the simulation. The silumation was run with position restrained on hexamer units with force constant of 1000 KJ/mol/nm2.
Are we missing any point in the mdp parameters or on restrian? We are unable to figure it out.
Thanks in advance.
Best regards
Devesh