[gmx-users] The molecular structure

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> 
> the molecular structure : bond length, bond angle, dihedral angle ....
> 
> the bond length, bond angle are easily determined..
> but the dihedral angle are hard to control...
> 

Are you looking to control (i.e., restrain/constrain) these parameters, or 
measure them?

> with one set of the force field parameter, I could not get the exact
> structure of the molecule (not all of the dihedral  angles are the
> same , but bond length and bond angle are the same)
> 

I should think not!  All bonds are not created equal.  Maybe I'm just missing 
your meaning.  Are you missing a parameter for your molecule?  If so, you'll 
have to derive it, or at least use a comparable parameter.  Are you trying to 
make a measurement?  If so, you haven't provided enough information to get a 
very helpful reply.

> will it affect my rest of simulation severely?
> 

Depends on how you answer the above :)

-Justin

> Thanks
> Lin
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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