[gmx-users] com motion

[Anton Feenstra]

Mustafa Toprakçý wrote:
> Hi David,
> Yes, this is a complex. In the topology file I have given it as one 
> molecule under [molecules] header. I have manually placed the ligand
> and miniöized it using steep. I made two groups, proteýn and ligand
> then heated the temp of the ligand to 1000K while keeping the protein
> at 300K. After this I made 400ps. simulation. Here is my mdp file:

If you freeze the protein, the ligand simply may only have very little
space to move in. 400 ps, after all, isn't that long.

I did simulations of octane in a Cytochrome P450 enzyme, where the
binding cavity is many times larger than octane. Still, the mobility
of the octane is relatively low. It 'sticks' to certain places for
long times (~1n is no exception). My simulations were 10 ns, the
protein is ~450 residues.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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