[gmx-users] Umbrella Sampling tutorial

[shahab shariati]

Dear Justin

Thanks for your reply


If I place drug molecule within the water, can I use the same Pull code
parameters in the case drug molecule within lipid bilayer?

pull            = umbrella
pull_geometry   = position  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = CHOL_DOPC
pull_group1     = drg
pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 100      ; kJ mol^-1 nm^-2
pull_init1      = 0
pull_vec1       = 0 0 1

Best wishes