[gmx-users] com motion

[Anton Feenstra]

Mustafa Toprakçý wrote:
> Hi Anton,
> I almost understood the situation. As you say the binding cavity in my
> complex is very narrow. So it needs longer time first. Then I have to
> tether the protein not freeze. Increasing the temperature is not much
> affective bacause it goes to internal motion. Because there is no 
> temperature coupling for comm group option in the code. 
>  And I sould define protein as comm_group, this way ligand comm motion
> will be free.

That sounds about right. Still, even with the protein 'tethered' (ie,
with position restraints) and not frozen, your ligand might be very
tightly bound and have only very little mobility. You could consider to
use the 'pull' option to pull your ligand out of the binding cavity,
if you want to get an idea of the barriers and/or path involved.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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