From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Wed Jun 12 2013 - 11:01:23 CDT
Hello everyone,
I am running simulation for a system containing a large protein + ATP
embedded in lipid bilayer. While running equilibrium simulation with a few
constraints (Fixed atom, constraints and extraBonds). I get a very strange
error for which there was no solution discussed in NAMD-list.
The error is here,
FATAL ERROR: Bad global bond count!
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
[0] Stack Traceback:
[0:0] CmiAbort+0x95 [0xcb886d]
[0:1] _Z8NAMD_bugPKc+0x85 [0x57f793]
[0:2] _ZN10Controller16compareChecksumsEii+0x167 [0x90bbb1]
[0:3] _ZN10Controller21printDynamicsEnergiesEi+0x17 [0x9169d7]
[0:4] _ZN10Controller9integrateEv+0x13d [0x90ff93]
[0:5] _ZN10Controller9algorithmEv+0x5f8 [0x902b4e]
[0:6] _ZN10Controller9threadRunEPS_+0xe [0x917f8a]
[0:7] CthStartThread+0x29 [0xbde511]
[0:8] /lib64/libc.so.6 [0x3248641870]
[0] Stack Traceback:
[0:0] /Projects/namd2/bin/current/Linux64-multicore/namd2 [0xcb979d]
[0:1] CmiAbort+0xd3 [0xcb88ab]
[0:2] _Z8NAMD_bugPKc+0x85 [0x57f793]
[0:3] _ZN10Controller16compareChecksumsEii+0x167 [0x90bbb1]
[0:4] _ZN10Controller21printDynamicsEnergiesEi+0x17 [0x9169d7]
[0:5] _ZN10Controller9integrateEv+0x13d [0x90ff93]
[0:6] _ZN10Controller9algorithmEv+0x5f8 [0x902b4e]
[0:7] _ZN10Controller9threadRunEPS_+0xe [0x917f8a]
[0:8] CthStartThread+0x29 [0xbde511]
[0:9] /lib64/libc.so.6 [0x3248641870]
Thanks in advance,
Peterson
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