TCL forces and boundary conditions

From: Tyler Luchko (
Date: Tue Jun 06 2006 - 18:23:27 CDT


I have been trying to implement a harmonic restraint using tclForces
and have had some problems. Part way through the run NAMD will crash
with the error:

Stack Traceback:
   [0] CmiAbort+0x35 [0x73428d]
   [1] /NANO/tools/NAMD_2.6b1_Linux-amd64-TCP/namd2 [0x7367af]
   [2] ReceiveDatagram+0x86 [0x7368be]
   [3] /NANO/tools/NAMD_2.6b1_Linux-amd64-TCP/namd2 [0x736217]
   [4] /NANO/tools/NAMD_2.6b1_Linux-amd64-TCP/namd2 [0x736532]
   [5] /NANO/tools/NAMD_2.6b1_Linux-amd64-TCP/namd2 [0x736172]
   [6] /NANO/tools/NAMD_2.6b1_Linux-amd64-TCP/namd2 [0x73a8d3]
   [7] CcdRaiseCondition+0x76 [0x73b08e]
   [8] CcdCallBacks+0xd0 [0x73b168]
   [9] CsdScheduleForever+0x7a [0x738c5a]
   [10] CsdScheduler+0x1c [0x73a2ac]
   [11] _Z10slave_initiPPc+0x13 [0x4a174b]
   [12] _ZN7BackEnd4initEiPPc+0x32b [0x4a172b]
   [13] main+0x39 [0x49d679]
   [14] __libc_start_main+0xa9 [0x2a95c01b49]
   [15] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x52

------------- Processor 21 Exiting: Called CmiAbort ------------

                 Length mismatch!!

This appears part way through my simulation, depending on how often I
print to the log, what calculations I do and how many CPUs I run on.
I have not been able to find any information on what this error means
through searching the NAMD site or the web in general.

My system is relatively large and I am applying restraints to
approximately 1700 atoms out of 200,000. Since I thought this might
be too much for tclForces I tried to implement the same restraints in
tclBC. However, I need to calculate the center-of-mass and/or the
moment of inertia of two objects before applying the restraining
force. Since I can only loop through the atoms once in tclBC, this
approach does not work either.

Is tclForces is the only method that I can use to implement my
harmonic restraint? If so, what does the error message mean?

Thank you,


(_ Tyler Luchko Ph.D. Candidate _)
  _) Department of Physics University of Alberta (_
(_ Edmonton, Alberta, Canada _)
  _) 780-492-5519 <- NEW (_

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