From: Z (shenzldlut_at_gmail.com)
Date: Mon Oct 06 2014 - 11:20:41 CDT
Thank you for your advice!But when I modfiy the NAMD configuration file
as your advice, the error about parameter colvars is still happenning.I
do not why?
Thank you very much!
P.S.
This is a part of log file:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE AT STEP 1000
WRITING COORDINATES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART COORDINATES
The last position output (seq=1000) takes 0.004 seconds, 13.584 MB of
memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=1000) takes 0.002 seconds, 13.776 MB of
memory in use
REINITIALIZING VELOCITIES AT STEP 1000 TO 300 KELVIN.
FATAL ERROR: Setting parameter colvars from script failed!
[2] Stack Traceback:
[2:0] CmiAbort+0x6b [0xa28ed6]
[2:1] _Z8NAMD_diePKc+0x4a [0x50d5aa]
[2:2]
_ZN12CkIndex_Node32_call_scriptParam_ScriptParamMsgEPvP4Node+0x1a [0x8cc00a]
[2:3] CkDeliverMessageFree+0x30 [0x9ad260]
[2:4] _Z15_processHandlerPvP11CkCoreState+0x3c6 [0x9b2aaf]
[2:5] CmiHandleMessage+0x21 [0xa2a79d]
[2:6] CsdScheduleForever+0x5f [0xa2c642]
TCL: Setting parameter colvars to on
FATAL ERROR: Setting parameter colvars from script failed!
Z
E-mail：shendlut_at_gmail.com
在 2014/10/6 23:01, Jérôme Hénin 写道:
> You have a "minimize" command before "colvars". Colvars should come first.
>
> Jerome
>
> On 6 October 2014 16:47, Z <shenzldlut_at_gmail.com
> <mailto:shenzldlut_at_gmail.com>> wrote:
>
> I try to change the colvar configuration file to unix format by
> doc2unix.However, the error which is about setting parameter
> colvars from script failed still occur.I do not konw which problem
> can also lead to this error.Can you help me?
> Thank you!
>
> Z
> E-mail：shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>
> 2014/10/6 20:03, Giacomo Fiorin :
>>
>> Branko is right, the newline issue on Windows is specific to
>> colvars or other components that have their own parsers.
>>
>> On Oct 6, 2014 8:01 AM, "Z" <shenzldlut_at_gmail.com
>> <mailto:shenzldlut_at_gmail.com>> wrote:
>>
>> OK!Thank you!
>> This is my configuration file:
>>
>> structure mem_50.psf
>> coordinates mem_50.pdb
>> set outputname mem_50
>>
>> set temperature 300
>>
>> # Input
>> paraTypeCharmm on
>> parameters par_all27_prot_lipid.prm
>>
>> temperature $temperature
>>
>> # Periodic Boundary conditions
>> cellBasisVector1 55.0 0.0 0.0
>> cellBasisVector2 0.0 55.0 0.0
>> cellBasisVector3 0.0 0.0 95.0
>> wrapWater on
>> wrapAll on
>> margin 3
>>
>>
>> # Force-Field Parameters
>> exclude scaled1-4
>> 1-4scaling 1.0
>> cutoff 12.
>> switching on
>> switchdist 10.
>> pairlistdist 14.5
>>
>>
>> # Integrator Parameters
>> timestep 1
>> nonbondedFreq 2
>> fullElectFrequency 4
>> stepspercycle 20
>>
>> #PME
>>
>> PME yes
>> PMEGridSpacing 1.0
>>
>>
>> # Constant Temperature Control
>> langevin on
>> langevinDamping 5
>> langevinTemp $temperature
>> langevinHydrogen no
>>
>>
>> # Constant Pressure Control
>> if {1} {
>> useGroupPressure yes
>> useFlexibleCell no
>> useConstantArea no
>>
>> langevinPiston on
>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> langevinPistonPeriod 1000.0
>> langevinPistonDecay 500.0
>> langevinPistonTemp $temperature
>> }
>>
>>
>> # Output
>> outputName $outputname
>> restartfreq 1000 ;# 500steps = every 1ps
>> dcdfreq 1000
>> outputEnergies 1000
>> outputPressure 1000
>> rigidBonds all
>> rigidTolerance 0.0005
>>
>> # Fixed Atoms Constraint (set PDB beta-column to 1)
>> if {1} {
>> fixedAtoms on
>> fixedAtomsFile mem_fix.pdb
>> fixedAtomsCol B
>> }
>>
>>
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>> if {1} {
>> tclForces on
>> set waterCheckFreq 10
>> set allatompdb mem_50.pdb
>> tclForcesScript addforce.tcl
>> }
>>
>>
>> if {1} {
>> tclBC on
>> tclBCScript {
>> set sphereCenter "0.0 0.0 0.0"
>> set sphereRadius 10.0
>> set maxForce 5.0
>> set pdbSource mem_50.pdb
>> set tclBCScript force.tcl
>> source $tclBCScript
>> }
>> }
>>
>>
>> if {1} {
>> minimize 1000
>> reinitvels $temperature
>> }
>>
>> colvars on
>> colvarsConfig Distance.in
>>
>> firsttimestep 22000
>> run 2000000
>>
>> Z
>> E-mail：shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>>
>> 2014/10/6 19:27, Giacomo Fiorin :
>>>
>>> Looks like the NAMD keyword isn't being recognized
>>> properly. It would be better to look at the entire NAMD
>>> configuration file.
>>>
>>> On Oct 6, 2014 6:54 AM, "Z" <shenzldlut_at_gmail.com
>>> <mailto:shenzldlut_at_gmail.com>> wrote:
>>>
>>> The colvars configuration as a separate file(.in
>>> format).In my NAMD config file ,the colvers is been
>>> written like this:
>>>
>>> colvars on
>>> colvarsConfig Distance.in
>>>
>>> firsttimestep 22000
>>> run 2000000
>>>
>>> Z
>>> E-mail：shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>>>
>>> 2014/10/6 18:45, Giacomo Fiorin:
>>>>
>>>> Do you supply the colvars configuration as a separate
>>>> file or as part of the NAMD configuration file?
>>>>
>>>> On Oct 6, 2014 6:26 AM, "Z" <shenzldlut_at_gmail.com
>>>> <mailto:shenzldlut_at_gmail.com>> wrote:
>>>>
>>>> Dear all,
>>>> I want to use ABF to calculate PMF,so I am running
>>>> simulation with colvars. However, the NAMD2.8 said :
>>>>
>>>> TCL: Setting parameter colvars to on
>>>> FATAL ERROR: Setting parameter colvars from script
>>>> failed!
>>>>
>>>> FATAL ERROR: Setting parameter colvars from script
>>>> failed!
>>>>
>>>> FATAL ERROR: Setting parameter colvars from script
>>>> failed!
>>>>
>>>> FATAL ERROR: Setting parameter colvars from script
>>>> failed!
>>>>
>>>> FATAL ERROR: Setting parameter colvars from script
>>>> failed!
>>>>
>>>> my colvars flie :
>>>> colvarsTrajFrequency 100
>>>> colvarsRestartFrequency 1000
>>>>
>>>> colvar {
>>>> name IonDistance
>>>>
>>>> width 0.1
>>>>
>>>> lowerboundary -45.6
>>>> upperboundary 45.6
>>>>
>>>> lowerWallConstant 10.0
>>>> upperWallConstant 10.0
>>>>
>>>> distanceZ {
>>>> main {
>>>> atomsFile ./main_atom.pdb
>>>> atomsCol B
>>>> atomsColValue 1.0
>>>> }
>>>> ref {
>>>> atomsFile ./ref_atom_2.pdb
>>>> atomsCol O
>>>> atomsColValue 1.0
>>>> }
>>>> }
>>>> }
>>>>
>>>> abf {
>>>> colvars IonDistance
>>>> fullSamples 100
>>>> hideJacobian
>>>> }
>>>>
>>>> I want to know which parameter has problem?
>>>> Thanks!
>>>>
>>>> P.S.
>>>> There are tclForces parameters in my conf flie.
>>>>
>>>> --
>>>> Z
>>>> E-mail：shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>>>>
>>>
>>
>
>
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