From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Nov 08 2017 - 05:40:19 CST
Hello Abhaysinh, the most recent versions of Colvars (e.g. nightly builds)
should be able to read Windows text files directly.
Also, please try to be more precise in managing the versions of NAMD: you
wrote that you used 2.12, but the output looks from 2.11.
Giacomo
On Wed, Nov 8, 2017 at 6:12 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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]
>>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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