[gmx-users] coarse grain dynamics

[Nuno Azoia]

Hi there!

I never worked with coarse grain simulations, but if you used a coarse
grain methodology you didn't include all the atoms, so you didn't
included hydrogens. So now you can not see them, of course. They are not
there.

If you need to "know the hydrogen bond interactions" you need to do some
"all atoms" simulation, not coarse grain.

Nuno Azoia

On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
> Dear Gromacs Users,
> 
> I have done coarse grain simulation for 2 peptides in bilayer for
> 1000ns, and now i would like to know the hydrogen bond interactions
> between these two peptides. Please let me know how to do this, i can
> visualize the trajectory in VMD, but unable to calculate the hydrogen
> bonding distance and the hydrogen bonds existing..
> 
> Thanks
> 
> Ram

-- 
Nuno Gonçalo Azoia Lopes
 
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