[gmx-users] pull code Umbrella

[virginia miguel]

Hi All, I am trying to run a pulling md for umbrella sampling of the partition of  two organic molecules into the center of a bilayer using the following mdp options:  

  pull                     = umbrella
  pull_geometry            = cylinder
  pull_r1                  = 1.4
  pull_r0                  = 1.9
  pull_dim                 = N N Y
  pull_start               = yes          ; define initial COM distance > 0
  pull_init1               = x
  pull_init2               = x
  pull_ngroups             = 2
  pull_group0              = DPP
  pull_group1              = UNO
  pull_group2              = DOS
  pull_vec1                = 0 0 1
  pull_vec2                = 0 0 1
  pull_nstxout             = 1000
  pull_nstfout             = 1000
  pull_rate1               = -0.001        ; 0.001 nm per ps = 1 nm per ns
  pull_k1                  = 1000          ; kJ mol^-1 nm^-2  
  pull_rate2               = -0.001        ; 0.001 nm per ps = 1 nm per ns
  pull_k2                  = 1000          ; kJ mol^-1 nm^-2  
                                                                                         


the thing is that in three md steeps, the molecules are in the center of the bilayer, whe they are supposed to move 1 nm per ns ...I have used these options before but using pull_geometry=distance and had no trouble, but now I do not know what  am I doing wrong...if some one could give me a hint, I would appreciate it. Regards, Virginia. Dra. Virginia Miguel
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