From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Nov 08 2017 - 05:12:12 CST
Hi,
This could be a problem with a Windows-style end-of-line. Please try
processing the colvars input with the dos2unix utility before running.
Jerome
On 8 November 2017 at 04:46, Abhaysinh Gaikwad <ahgaikwa_at_aggies.ncat.edu>
wrote:
> 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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