[gmx-users] bad bond in polymer

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 13 02:36:21 CEST 2009

nicegromacs wrote:
> Hi gmx-users,
> I am building a polymer and I've added the monomer unit to the 
> .rtp file. The final structure appears with an undesired bond between 
> the monomer units at the extremes of the polymer.
> How can I prevent the monomers at the end forming the bond?

Bonds that appear in visualization software are separate from bonds that exist 
in the topology.  Programs like VMD guess where bonds should be based on atomic 
distances, which may or may not correspond to reality.

Be assured that the only true bonds are the ones you have defined in the topology.


> I have read other post like 
> http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html  but  
> can not avoid this problem .
> Thank you in advance
> veduardo.
> Lab. de  Fisicoquímica Molecular
> Facultas de Ciencias
> Universidad de Chile
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list