[gmx-users] How to write pull code in umbrella sampling
lvqingjiejie at 163.com
Sat Apr 8 02:56:43 CEST 2017
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
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