[gmx-users] AFM by using mdrun in gromacs

anirban polley polley.anirban at gmail.com
Wed Jul 30 11:07:47 CEST 2008

         I want to pull  a protein from a DPPC lipid bilayer.  It is written
in manual that it can be done by including pull.ppa and pull.ndx with the
         Now my question is how to write pull.ppa and pull.ndx.Can you tell
me which parts I have to take care to make group in index file?
 Can you tell me how to create pull.ndx properly, because during the making
of index file by giving make_ndx, I have confused which  elements  should be
grouped ( two tails of the DPPC molecule or tails of protein molecule).
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