[gmx-users] Using COM pulling and Enforced Rotations together

[Abhi Acharya]

Hello Gromacs users,

I would like to use COM pulling and Enforced rotations simultaneously on a
single domain. Is it possible at all to do so? I tried to run an
simulation; it ran fine without errors, but analysis indicates COM pulling
may not have worked properly although the domain was rotated by the correct
angle. I used the following parameters.

The .mdp portion is as follows:

; COM PULLING
; Pull type: no, umbrella, constraint or constant-force
pull                     = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry            = direction
; Select components for the pull vector. default: Y Y Y
pull_dim                 = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1                  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0                  = 1.5
pull_constr_tol          = 1e-06
pull_start               = no
pull_nstxout             = 10
pull_nstfout             = 1
; Number of pull groups
pull_ngroups             = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0              = KH-domain
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = GD-domain
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = -0.11353457 -0.35303290 0.92869676
pull_init1               = 0.0
pull_rate1               = -0.0002667
pull_k1                  = 1000
pull_kB1                 = 1000

; ENFORCED ROTATION
; Enforced rotation: No or Yes
rotation                 = Yes
; Output frequency for angle, torque and rotation potential energy for the
whole group
rot_nstrout              = 100
; Output frequency for per-slab data (angles, torques and slab centers)
rot_nstsout              = 1000
; Number of rotation groups
rot_ngroups              = 1
; Rotation group name
rot_group0               = GD-C-alpha
; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2,
rm2-pf, flex, flex-t, flex2, flex2-t
rot_type0                = flex
; Use mass-weighting of the rotation group positions
rot_massw0               = no
; Rotation vector, will get normalized
rot_vec0                 = -0.11353457 -0.35303290 0.92869676
; Pivot point for the potentials iso, pm, rm, and rm2 (nm)
rot_pivot0               = 2.832087779  4.635125870   0.00000000
; Rotation rate (degree/ps) and force constant (kJ/(mol*nm^2))
rot_rate0                = -0.0174
rot_k0                   = 400
; Slab distance for flexible axis rotation (nm)
rot_slab_dist0           = 1.5
; Minimum value of Gaussian function for the force to be evaluated (for
flex* potentials)
rot_min_gauss0           = 0.001
; Value of additive constant epsilon' (nm^2) for rm2* and flex2* potentials
rot_eps0                 = 0
; Fitting method to determine angle of rotation group (rmsd, norm, or
potential)
rot_fit_method0          = norm
; For fit type 'potential', nr. of angles around the reference for which
the pot. is evaluated
rot_potfit_nsteps0       = 21
; For fit type 'potential', distance in degrees between two consecutive
angles
rot_potfit_step0         = 0.25


Thanks in advance.

Regards.
Abhishek Acharya