[gmx-users] rotational barrier

[Dallas Warren]

>I working with phenylacetylene oligomers in which the phenyl rings are 
>connected by alkyne linkages.
>untitled.bmp
>I want to introduce rotation barriers to keep the phenyl rings coplanar.
>is it possible to introduce a dihedral around the single bond that 
>connects the phenyl ring
>to the alkyne carbon? if yes, how can i define it in gromacs?

Same as you define any other dihedral, how it is done depends a bit on the 
forcefield used.  Chapter 5 covers the formatting used in the topology 
files, probably 5.6 is the section of most interest, and the theory is in 
4.2.10
   To keep things coplanar you may have to use an improper ?
Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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