[gmx-users] COM Pulling

Raj princecrusial05 at gmail.com
Fri Jun 29 15:03:04 CEST 2012

HI , I have been performing SMD after reading bevan lab tutorial. The
tutorial was very informative in basic aspects. Now I have my ligand inside
the protein and I wan to pull it out in a specific direction. I applied
force separately along the X, Y and Z axis . In which none of the pull seems
to be proper. In the sense the ligand didn't come through the already
predicted channel. So my question is can i specify the direction of the pull
by mentioning the amino acid residues lined along the channel of the protein
? if i can what is the modification I should do to achieve the objection.
Thanks in advance 

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