Re: Parameter colvars

From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
Date: Mon Oct 06 2014 - 15:56:18 CDT

Is there a reason you are using namd2.8? It did have colvars implemented
(so not the cause of your problem) but the most recent version is
NAMD2.10b1, which has much improved colvars. I think 2.8 may have had some
bugs, although Jerome and Giacomo would know better whether they would
affect a distanceZ ABF calculation.

Grace

On Mon, Oct 6, 2014 at 4:25 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Actually, you still are issuing "run" before issuing "colvars".
>
> On Mon, Oct 6, 2014 at 12:20 PM, Z <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
>>
>> 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> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
>
> --
> 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
> https://icms.cst.temple.edu/members.html
> http://giacomofiorin.github.io/
>
>

-- 
Grace Brannigan, Ph.D.
Assistant Professor
Center for Computational and Integrative Biology (CCIB) &
Department of Physics
Rutgers University, Camden, NJ
(856)225-6780
www.branniganlab.org

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