[gmx-users] Change to umbrella sampling pull code

Nash, Anthony a.nash at ucl.ac.uk
Wed Aug 12 18:19:58 CEST 2015

Dear all,

This is the first time I¹ve ran pull code (for umbrella sampling) since
the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in
the .mdp key-value parameters. Could I have a sanity check on the values
below. Also, given that I want a harmonic potential between the two
groups, does it matter which index group is assigned to the respective
Œpull-groupN-name¹ key?

Note: my reaction coordinate was defined initially following the
trajectory between two minima during a meta-dynamics MD simulation. That
too was distance based.

;Pull code
pull            = umbrella
pull-geometry   = distance
pull-dim        = Y Y Y
pull-start      = yes
pull-ngroups    = 1
pull-group1-name = ZINC
pull-group2-name = CARBONYL
pull-coord1-init = 0
pull-coord1-rate = 0
pull-coord1-k = 1000
pull-nstxout    = 1000      ; every 2 ps
pull-nstfout    = 1000      ; every 2 ps

Many thanks

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