[gmx-users] Umbrella Sampling settings

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Jul 11 22:21:07 CEST 2013


I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window.
Some mdp file settings for running US, as I found in US tutorial are :
; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = yes 
pull_ngroups    = 1
pull_group0     = Chain_B 
pull_group1     = Chain_A 
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 4000      ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 2 ps
pull_nstfout    = 1000      ; every 2 ps

But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling!

Would you please help me in this about?
Thanks in advance for your suggestions.


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