[gmx-users] Problems with AFM pulling

lvcp lvcp at ustc.edu
Tue Apr 18 10:12:35 CEST 2006

     I am trying to simulate the pulling process of a protein by Gromacs 3.2.0. However, when executing the command "mdrun -v -s pull.mdp -o pull_1.tpr -c afterpull -pi pull.ppa -pn pull.ndx", the program only back off the pullout.ppa and pull.pdo with no computing done.     I don't know what's the reason. Is there some problem with my pull.ppa file? Content of the file is:       verbose            = no       runtype            = afm       group_1            = Pull_C       reference_group    = Pull_N       reftype            = com       pull_dim            = N N Y
       afm_rate1                = 0.001        afm_k1                   = 1000       afm_dir1                 = 0.0 0.0 1.0       afm_init1                = 0.0 0.0 0.0   Thanks for any message.
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