[gmx-users] the pull code

diana p diana64mp at gmail.com
Tue Aug 9 08:33:06 CEST 2016

Dear all

I am using the pull code in Gromacs 4.6.5 to calculate the PMF in one
direction (z) between two graphene sheets in the inter-sheet separation ,
ranging from 5.0 to 0.3 nm. I run EM and NPT by using .mdp files. When i
run the  continuous pulling simulation, i seen they are at the current
location and no movement towards each other!
The pull parameters are the following:

;Pull code

pull = umbrella

pull_geometry = direction_periodic   ; simple distance increase

pull_dim = N N Y

pull_start = yes       ; define initial COM distance > 0

pull_ngroups = 1

pull_group0 = GRA 1

pull_group1 = GRA 2

pull_rate1 = 0.01      ; 0.01 nm per ps = 10 nm per ns

pull_k1 = 1000      ; kJ mol^-1 nm^-2

I would be more than pleased if someone could guid me.
Thank You in advance

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