[gmx-users] Erik Lindahl,md_hole process!!

[nanyu101]

Dear Dr.Erik Lindahl,
  Thanks for your prompt reply.I just want to know the process of making hole.
First,I should minimize my bilayer system such as dppc128.pdb or popc128a.pdb downloaded from Dr.Tieleman's web.
Second, I know my cylinder's radius.I run make_hole.pl to create a hole as big as my cylinder.
Third.I create my run.mdp and hp.mdp just as md_hole tutorial told.And then run grompp -f run.mdp -o insert.tpr -c bilayer.pdb -r bilayer.pdb -p bilayer.top
mdrun -v -hole -holep hp.mdp -deffnm insert....
If I manage the processes above,I can put my cylinder into my hole.
cat protein.pdb bilayer.pdb > ion_bilayer.pdb.

Dr.Erik Lindahl,are there something wrong?If not,how can I improve my technology in dynamics and minimization?

Thanks a lot.

Best wishes,
Xianhui Wu
______________________________________

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