[gmx-users] Force magnitude in SMD pull_geometry options

[Magdalena von Essen]

Dear Gromacs users,
I have a question about the two different pull geometry options; 
direction and direction_periodic.
I have previously performed SMD constant force pulling (gromacs 
ver.4.5.5) with the following mdp setting:
; Pressure coupling is on whole system in two groups
Pcoupl                     = Berendsen
pcoupltype            = isotropic
tau_p                        = 1.0     1.0
compressibility    = 4.5e-5     4.5e-5
ref_p                         = 1.0     1.0
refcoord_scaling  = all
...
; Pull code
pull                        = constant_force
pull_geometry  = distance
pull_vec1            = 0.0     0.0     5.5
pull_ngroups     = 1
pull_group0       = a_5
pull_group1       = a_2733
pull_k1                 = -180.7        ; [kJ/(mol.nm)^-1], 300 pN
/
/With versions 4.6.x the same setting however crashes with the following 
error message:/
"...gromacs Distance of pull group 1 (5.492401 nm) is larger than 0.49 
times the box size...".

/I have changed the pull geometry to distance_periodic and hence the 
pressure conditions to semiisotropic (off in z directions)/
/Pcoupl                     = Berendsen
pcoupltype            = isotropic
tau_p                        = 1.0     0
compressibility    = 4.5e-5     0
ref_p                         = 1.0    0
refcoord_scaling  = all
...
; Pull code
pull                        = constant_force
pull_geometry  = distance_periodic
pull_vec1            = 0.0     0.0     5.5
pull_ngroups     = 1
pull_group0       = a_5
pull_group1       = a_2733
pull_k1                 = -180.7        ; [kJ/(mol.nm)^-1], 300 pN

This pulling goes over the half of the box. The protein unfolding 
however goes much faster compared to the same force magnitude unfolding 
observed in the first setting.
Comparable unfolding dynamics was then found with the following force 
magnitudes (system size approx. 400,000 atoms):
isotropic setting + distance geometry -> force 300pN
semiisotropic setting + distance_periodic geometry -> force 50pN

(In much smaller system of approx. 40,000 atoms, the pulling force 
magnitude and the unfolding dynamics were comparable).
I did not find any difference comparing the system pressure, temperature 
or water molecule velocity distributions.

My question concerns the cause of such large difference in the force 
between the two systems?
And can I check somehow that the system performs well?

Thanks guys for your time.
Cheers,
Magdalena