[gmx-users] Improper dihedral and trans double bond

[Anton Feenstra]

Patel Ronak Y wrote:

> Dear all,
> 
> I wish to simulate lipid molecule having trans double (CH2-CH1=CH1-CH2)
> bond in the hydrocarbon tail.
> 
> Do I have to enter improper dihedral to maintain planarity of this double
> bond in the rtp file (the way we maintain planarity for cis double bond).

Yes. Be aware that an improper with a reference angle of 180 degrees doesn't
work well (due to the periodicity of the angle), and you should define it
with a different order of atoms that will allow an angle close to 0.


-- 
Groetjes,

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