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