[gmx-users] Pulling code

Andres Ortega og_andres15 at hotmail.com
Sun Mar 23 02:49:04 CET 2014

Dear Gromacs Users, 

My system consist of a proteins ( membrane channel) and a drug (DOX) 
and i am trying to run a pull_md in order to force the drug to permeate the
channel, but, 
the channel size and the durg molecule are closed, so i've been reading , i
dont know if i should use constraint to the protein, i think i should in
order to facilitated the permeation for my PMF calculation, 

i have also read other post about the pulling code
i decided to used cylinder like this 

; Pull code
pull            = umbrella
pull_geometry   = cylinder  ; 
pull_vec1       = 0 0 -1 ; 1 or -1 ??
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = DOX 
pull-r1			= 1.0 
pull-r0 		= 1.0 
pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2

my other question is about the pull-pbcatom1: due to some person presented
problems, this should be in the middle of the channel, or select group0 a
central atom in the channel , 
i would really thank all your suggestions and tips, thank you in advance

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