RMSD colvar not working in NAMD2.12 Linux version

From: Abhaysinh Gaikwad (ahgaikwa_at_aggies.ncat.edu)
Date: Tue Nov 07 2017 - 21:46:28 CST

I am using RMSD colvar and it runs successfully in NAMD2.12 (Windows
version). However, when I try to run the same simulation in Linux 64bit
multicore GPU cuda version (Nvidia) it does not run. It gives an error show
below. How can I remedy the situation.

colvars: ------------------------------------------------------------
----------

colvars: Initializing the collective variables module, version 2015-09-16.

colvars: Using NAMD interface, version 2015-07-24.

colvars: ------------------------------------------------------------
----------

colvars: Reading new configuration from file "Sim1colvar_v8.conf":

colvars: # indexFile = "" [default]

colvars: # analysis = off [default]

colvars: # colvarsTrajFrequency = 1000

colvars: # colvarsRestartFrequency = 1000

colvars: # colvarsTrajAppend = off [default]

colvars: ------------------------------------------------------------
----------

colvars: Initializing a new collective variable.

colvars: # name = RMSD

colvars: Initializing a new "rmsd" component.

colvars: # componentCoeff = 1 [default]

colvars: # componentExp = 1 [default]

colvars: # period = 0 [default]

colvars: # wrapAround = 0 [default]

colvars: Initializing atom group "atoms".

colvars: # indexGroup = "" [default]

colvars: # psfSegID = [default]

colvars: # atomsFile = Sistamp_restrainedpull.pdb

colvars: # atomsCol = O

colvars: # atomsColValue = 9999

colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]

colvars: # enableForces = on [default]

colvars: # centerReference = off [default]

colvars: # rotateReference = off [default]

colvars: # enableFitGradients = on [default]

colvars: Error: keyword "" is not supported, or not recognized in
this context.

colvars: Error setting up atom group "atoms".

colvars: If this error message is unclear, try recompiling with
-DCOLVARS_DEBUG.

FATAL ERROR: Error in the collective variables module: exiting.

[0] Stack Traceback:

  [0:0] CmiAbort+0x41 [0xefde44]

  [0:1] _Z8NAMD_diePKc+0x93 [0x64a6c3]

  [0:2] _ZN16colvarproxy_namd5errorERKSs+0x938 [0xaddd18]

  [0:3] _ZN12colvarmodule10atom_group5parseERKSsPKc+0x2b56 [0x9e5006]

  [0:4] _ZN6colvar3cvc11parse_groupERKSsPKcRN12colvarmodule10atom_groupEb+0x116
[0xa47936]

  [0:5] _ZN6colvar4rmsdC1ERKSs+0x13d [0xa66cbd]

  [0:6] _ZN6colvarC1ERKSs+0xac8b [0x9aa22b]

  [0:7] _ZN12colvarmodule13parse_colvarsERKSs+0x154 [0xa9f964]

  [0:8] _ZN12colvarmodule12parse_configERSs+0x21f [0xa9d96f]

  [0:9] _ZN12colvarmodule16read_config_fileEPKc+0x2a2 [0xa9d202]

  [0:10] _ZN16colvarproxy_namdC1Ev+0x7e5 [0xad30b5]

  [0:11] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x287 [0x6bc357]

  [0:12] _ZN4Node7startupEv+0x23d [0xb8a85d]

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