[gmx-users] How to write pull code in umbrella sampling

[Qing Lv]

Dear Colleagues,


I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file.
Below is the pull code from the tutorial of Dr. Justin Lemkul :
define      = -DPOSRES_B ; (Why ??)
; Pull code             
pull                    = yes       
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_B
pull_group2_name        = Chain_A
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord1_rate        = 0.0
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0



Conformations in Justin's tutorial are from steered MD. However, my conformations are not from SMD, and I have not done SMD on this system. So, how to define pull_group1 and pull_group2? And pull_coord1_geometry still set to "distance" ?
Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? Why?
Any one can provide a template of pull code for such simulations?


Thanks a lot
Qing Lv