[gmx-users] questions about SMD simulation of P450 for Anton

nk yx nkyx at hotmail.com
Tue Apr 15 14:04:01 CEST 2003

   When I do Steered MD simulation of P450 complex using Gromacs, I found 
the spring force constant has a great influnce on the pull direction. When 
i set the force constant=1000,the substrate exits along the I helix( 
predefined pull direction); When i use forceconstant=1500 or 500, the 
substrate exit from the B-C loop,  greatly deviating from the predefined 
direction. I don't know why.
  I don't know whether I correctly set up the pull direction. I define the 
pull direction on the z-axis by the center of mass of two groups,which one 
group is the substrate and the other is four backbone C atomes at the mouth 
of exit channel.
  Could you give me some advice?

Best wishes,

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