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.
-Justin
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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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