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

[Anton Feenstra]

nk yx wrote:
> Hi,Anton
>   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.


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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