problem with gpu namd 2.9b3

From: Peter Jones (
Date: Thu Apr 19 2012 - 04:30:42 CDT


I'm trying to run a simulation using Namd 2.9b3 on a cluster with gpu acceleration; its a continuation of a job that was running on another machine. Namd starts ok, prints out the energies for step 0, and then prints-

LDB: ============= START OF LOAD BALANCING ============== 11.8193
LDB: ============== END OF LOAD BALANCING =============== 11.8194
LDB: =============== DONE WITH MIGRATION ================ 11.8197
0:961(5) atom 32894 found 2 exclusions but expected 3
0:1042(50) atom 40634 found 2 exclusions but expected 3

followed by a long list of messages similar to the last two lines. This is followed by a list of errors regarding RATTLE constraint failures and then termination. I'm new to gpu-accelerated NAMD and I do not have any idea what is wrong here, any help would be greatly appreciated,


Kind Regards,
Peter Jones

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