From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Oct 06 2014 - 10:01:52 CDT
You have a "minimize" command before "colvars". Colvars should come first.
Jerome
On 6 October 2014 16:47, Z <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
>
> 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> 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
>>
>> 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> 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
>>>
>>> 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> 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
>>>>
>>>>
>>>
>>
>
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