[gmx-users] the qusition about the AFM

[zjim]

hi
I use gromacs to calculate the force to pull a ligind out of the protein. the pull.ppa file is as follow.
  verbose                  = no
 runtype                   = afm
 group_1                  = NOJ
 reference_group       = Protein
 reftype                    = com
 reflag                     = 1
 pulldim                  = N Y N
 afm_rate1                = 0.005
 afm_k1                   = 0.01
 afm_dir1                 = 0.0 -1.0 0.0
 afm_init1                = 0.334 -0.223 0.445
when i  change the value of "afm_init1"or " afm_rate1" or  " afm_k1" ,the output force in "pull.pdo" file keeps same, yet i think the force should be changed. that is the quiestion.can some give me an explaination ?
thank you very much!













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