Bad global bond count

From: Fugui (
Date: Mon May 06 2013 - 15:26:52 CDT

Dear NAMD users:
I used annealing MD to convert coarse grained structure into all-atom structure. Firstly, i got an all-atom structure using VMD from an coarse grained structure and an all-atom structure (before MD). However, there are several long C-C bonds, and when i tried to run an annealing MD, it always died, and i got the information: Bad global bond cout. I tried to increase the box size and increase the MARGIN parameter, but it does not work. It is suggested that splitPatch parameter can solve the problem. I set splitPatch to Hydrogen, but i still got the same error information. It may works to set the long C-C atoms as splitPatch. However, i do not know how to set splitPatch value, can anyone give me some suggestions?

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