[gmx-users] about the bond connection between different groups

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 22 08:22:37 CEST 2009

Hi He Yang, Justin,

>> You have said bonds between distinct molecules require a merged topology.
>> Is
>> there any introduction in the manual or Do you have any example about the
>> merged topology?
> A merged topology contains multiple moleculetype definitions in one
> topol.top. Discussions are in the archives.

Bonds can only be defined within moleculetypes, not between them. So
you'll need to combine moleculetypes to create a bond between groups.
For this you have to renumber all atoms from one of the moleculetypes,
starting at N+1, with N being the number of the last atom of the first
moleculetype. You also have to renumber the indices for all other
blocks ([bonds], [angles], etc...). Then combine the blocks and
finally add the new bond. If it is a proper bond, you should also
consider adding the angles and dihedrals involved in the interaction.
Note again, merging to create a bond does not mean adding multiple
moleculetypes in one topol.top!



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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