Dear all,

Is there anyway to apply pulling force or shear rate on either system or protein?

If possible, could you please tell me the method or needed modification step by step?

Many thanks in advance,

Best

Dear all,

Is there anyway to apply pulling force or shear rate on either system or protein?

If possible, could you please tell me the method or needed modification step by step?

Many thanks in advance,

Best

Hi,

maybe the mdp option ‘deform’ Molecular dynamics parameters (.mdp options) — GROMACS 2021.1 documentation

is doing what you look for.

Best regards

Alessandra

Hi,

one way to shear a fluid solvant is to restrain two layers of solvant molecules or solid walls, one close to z=0 and one close to z=Lz, and then utilize an auxillary free-energy calculation to interpolate between the reference restraints and the same restraints ofset by +/- delta along x; that will cause a deformation that in turn will produce a steady shear rate, given that lambda is allowed to vary in [0,infinity). You may want to use pbc along xy alone.

If you want to apply a constant force to the whole system (or to every residue of some kind), you can use Non-equilibrium MD acc-grps and accelerate.