From: Z (shenzldlut_at_gmail.com)
Date: Mon Oct 06 2014 - 22:05:28 CDT
Thanks for your patient!
So, I should run "run" command first and run "colvars" command second.
Like this :
run 2000000
colvars on
colvarsConfig Distance2.in
Is it right?
Alternatively, do the parameter of NAMD configuration file before
colvars command has some wrong?
Z
E-mail：shendlut_at_gmail.com
2014/10/7 4:25, Giacomo Fiorin :
> Actually, you still are issuing "run" before issuing "colvars".
>
> On Mon, Oct 6, 2014 at 12:20 PM, Z <shenzldlut_at_gmail.com
> <mailto:shenzldlut_at_gmail.com>> wrote:
>
> 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 <mailto:shendlut_at_gmail.com>
>
> 2014/10/6 23:01, Jérôme Hénin :
>> 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>
>>>>>
>>>>
>>>
>>
>>
>
>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213 <tel:%2B1-215-204-4213>
> https://icms.cst.temple.edu/members.html
> http://giacomofiorin.github.io/
>
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