Re: Parameter colvars

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 06 2014 - 15:25:06 CDT

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/

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:54 CST