GROMACS version: 2018.8
GROMACS modification: Yes/No
Dear Justin,
I want to evaluate a PMF using umbrella sampling for rotating an atom around a dihedral angle. For example; C1, C2, C3, C4 atoms constructed a dihedral and I want to rotate C1. Would you please give some keywords for this purpose? I know how to calculated PMF based on distance (pulling), but how can I rotating an atom (around 360 degrees) and calculate the PMF. To calculate PMF, I want to define a reaction coordinate, ξ, an angle (dihedral rotation).
Best regards,
Ganj
pull-coord1-geometry = dihedral is probably what you want but I have never used it. Hopefully someone else will share their experience.
In case someone comes across this thread for reference, I think I got it after a lot of trial and error.
; Umbrella sampling parameters
pull = yes ;
pull-ngroups = 5 ;
pull-group1-name = atom_5 ;
pull-group2-name = atom_7 ;
pull-group3-name = atom_9 ;
pull-group4-name = atom_15 ;
pull-group5-name = atom_17 ;
pull-ncoords = 2 ;
pull-coord1-type = umbrella ;
pull-coord1-geometry = dihedral ;
pull-coord1-dim = Y Y Y ;
pull-coord1-k = 1000 ;
pull-coord1-start = no ;
pull-coord1-groups = 1 2 2 3 3 4 ; atoms 5 7 7 9 9 15
pull-coord1-init = -1.0472 ;
pull-coord2-type = umbrella ;
pull-coord2-geometry = dihedral ;
pull-coord2-dim = Y Y Y ;
pull-coord2-k = 1000 ;
pull-coord2-start = no ;
pull-coord2-groups = 2 3 3 4 4 5; atoms 7 9 9 15 15 17
pull-coord2-init = -1.0472 ;
I am trying to bias phi and psi. The atoms involved are (phi = 5 7 9 15) and (psi = 7 9 15 17). You need to define additional groups in your index file. For reference, this is my index file where I appended the groups “atom_5”, “atom_7”, so on and so forth:
[ atom_5 ]
5
[ atom_7 ]
7
[ atom_9 ]
9
[ atom_15 ]
15
[ atom_17 ]
17
Let me know if anyone needs additional assistance in defining dihedrals.