[gmx-users] questions about SMD simulation of P450 for Anton
feenstra at chem.vu.nl
Thu Apr 17 09:36:03 CEST 2003
nk yx wrote:
> 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?
Sorry, I have never used the pull options. The results sound very
suspicious, though. You might try pulling in vacuum, with otherwise
identical set-up, to check if you do what you think you do.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
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