[gmx-users] Soln to visualised long molecule bonds across box in VMD

Dallas Warren Dallas.Warren at monash.edu
Mon Jun 2 07:52:52 CEST 2014

When visualising a simulation with VMD, a significant number of people encounter an issue where the bonds, typically appearing when loading a trajectory on a starting structure (in which the bonds are correct), then being drawn across the box.  There are some extensive discussions on this emailing list on how to use trjconv to deal with the problem.

Additionally, someone recently posted to the VMD emailing list some possible solutions and thought this might be of interest/use to people here.


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

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