[gmx-users] rotational barrier

Dallas Warren dallas.warren at vcp.monash.edu.au
Fri Sep 17 02:14:39 CEST 2004

>I working with phenylacetylene oligomers in which the phenyl rings are 
>connected by alkyne linkages.
>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 
   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
When the only tool you own is a hammer, every problem begins to resemble a nail.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: untitled.bmp
Type: application/octet-stream
Size: 15894 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040917/7dd3ccd8/attachment.obj>

More information about the gromacs.org_gmx-users mailing list