From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 06 2014 - 07:03:38 CDT
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
>
> 在 2014/10/6 19:27, Giacomo Fiorin 写道:
>
> 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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