[gmx-users] Com pulling in reverse Z direction in SMD simulation..

Kalyanashis kalyan.chem.in at gmail.com
Thu Apr 24 11:22:34 CEST 2014


Dear all, 
  I am doing SMD simulation of a enzyme system and I have given the pull
option in Z direction. The com pulling options are given below,
;COM pulling
pull                     = umbrella
pull_geometry            = distance
pull_dim                 = N N Y
pull_r1                  = 1
pull_r0                  = 1
;pull_constr_tot          = 1e-6
pull_start               = yes
pull_nstxout             = 10
pull_nstfout             = 1
pull_ngroups             = 1
;name of reference group
pull_group0              = Protein
;pull_weights             = 0
;name of pull group
pull_group1              = UNK
;pull_weights             = 0
pull_vec1                = 0.0 0.0 -1
;ref. distance at t=0
;pull_init1               = -2.4477384   -1.0229216   -1.5900776
;rate of change of ref. gr. [nm/ps]
pull_rate1               = 0.0005
;force constant [KJ mol^-1 nm^-2]
pull_k1                  = 1586.747
;pull_kB1                =

Please kindly tell me, how can I do the same calculation in reverse Z
direction??
Thank you so much,
Kalyan....

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