Re: water equilibration

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Jun 08 2011 - 14:40:03 CDT

Neither. There needs to be a space between "if" and "{" in Tcl.

-Jim

On Wed, 8 Jun 2011, Gurunath Katagi wrote:

> Hi ..
> i needed a small clarification ..
> should it be
> if{0}
> exclude (options)
> or
> if{1} {
> exclude (options) , inorder to include for the calculation ?
>
> Thank you
> Gurunath
>
>
> On Tue, Jun 7, 2011 at 9:50 PM, johan strumpfer <johan.ks.uiuc_at_gmail.com>wrote:
>
>> Naresh,
>>
>> In the future, if someone asks you to post the whole error message it
>> is often useful to post all the lines that contain "ERROR". If you
>> read the log file you will see:
>> ERROR: 'exclude' is a required configuration option
>> ERROR: exclude defines: Electrostatic and VDW exclusion policy
>> ERROR: The following variables were set in the
>> ERROR: configuration file but are NOT VALID
>> ERROR: if{0}
>>
>> I.e. you have 2 errors: exclude needs to be defined, and if{0} needs
>> to be correct tcl syntax. Change "if{0}" to "if {0}" and add "exclude
>> none" to the config file.
>>
>> Cheers,
>> Johan
>>
>> ----------------------------------------------------------------
>> Johan Strumpfer (johanstr_at_ks.uiuc.edu)
>> Theoretical and Computational Biophysics Group
>> 3115 Beckman Institute
>> University of Illinois at Urbana-Champaign
>> 405 N. Mathews
>> Urbana, IL 61801, USA
>>
>>
>>
>> On Tue, Jun 7, 2011 at 12:15 PM, Narasimhan LOGANATHAN
>> <Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
>>> Hi,
>>> Thanks for the reply. Herewith, i aam posting the information in the
>> log file.
>>> And also the custom forcefield in X-plor format
>>>
>>> #############################################
>>> Log File
>>> #############################################
>>>
>>> Charm++: standalone mode (not using charmrun)
>>> Warning> Randomization of stack pointer is turned on in kernel, thread
>> migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space'
>> as root to disable it, or try run with '+isomalloc_sync'.
>>> Charm++: scheduler running in netpoll mode.
>>> Charm++> Running on 1 unique compute nodes (12-way SMP).
>>> Charm++> Cpu topology info:
>>> PE to node map: 0
>>> Node to PE map:
>>> Chip #0: 0
>>> Charm++> cpu topology info is gathered in 0.000 seconds.
>>> Info: NAMD 2.7 for Linux-x86_64
>>> Info:
>>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>>> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
>>> Info:
>>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>>> Info: in all publications reporting results obtained with NAMD.
>>> Info:
>>> Info: Based on Charm++/Converse 60202 for net-linux-x86_64-iccstatic
>>> Info: Built Wed Oct 13 11:38:08 CDT 2010 by jim on belfast.ks.uiuc.edu
>>> Info: 1 NAMD 2.7 Linux-x86_64 1 nanpc45.in2p3.fr accelrys
>>> Info: Running on 1 processors.
>>> Info: CPU topology information available.
>>> Info: Charm++/Converse parallel runtime startup completed at 0.00228715 s
>>> Info: 1.49471 MB of memory in use based on CmiMemoryUsage
>>> Info: Configuration file is water.conf
>>> TCL: Suspending until startup complete.
>>> ERROR: 'exclude' is a required configuration option
>>> ERROR: exclude defines: Electrostatic and VDW exclusion policy
>>> ERROR: The following variables were set in the
>>> ERROR: configuration file but are NOT VALID
>>> ERROR: if{0}
>>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>> [0] Stack Traceback:
>>> [0:0] CmiAbort+0x7b [0xb3ecb1]
>>> [0:1] _Z8NAMD_diePKc+0x62 [0x520802]
>>> [0:2] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73
>> [0xa0f199]
>>> [0:3] _ZN9NamdState14configListInitEP10ConfigList+0x3d9 [0x978d37]
>>> [0:4] _ZN9ScriptTcl9initcheckEv+0x5e [0x9e9a9c]
>>> [0:5] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x20 [0x9e6364]
>>> [0:6] TclInvokeStringCommand+0x91 [0xb6ca38]
>>> [0:7] namd2 [0xba2888]
>>> [0:8] Tcl_EvalEx+0x176 [0xba2ecb]
>>> [0:9] Tcl_EvalFile+0x134 [0xb9a8d4]
>>> [0:10] _ZN9ScriptTcl3runEPc+0x14 [0x9e5b82]
>>> [0:11] _Z18after_backend_initiPPc+0x22b [0x525053]
>>> [0:12] main+0x3a [0x524df2]
>>> [0:13] __libc_start_main+0xf4 [0x3dc541d994]
>>> [0:14] _ZNSt8ios_base4InitD1Ev+0x4a [0x5200fa]
>>> [0] Stack Traceback:
>>> [0:0] namd2 [0xb3f86d]
>>> [0:1] CmiAbort+0xb9 [0xb3ecef]
>>> [0:2] _Z8NAMD_diePKc+0x62 [0x520802]
>>> [0:3] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73
>> [0xa0f199]
>>> [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x3d9 [0x978d37]
>>> [0:5] _ZN9ScriptTcl9initcheckEv+0x5e [0x9e9a9c]
>>> [0:6] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x20 [0x9e6364]
>>> [0:7] TclInvokeStringCommand+0x91 [0xb6ca38]
>>> [0:8] namd2 [0xba2888]
>>> [0:9] Tcl_EvalEx+0x176 [0xba2ecb]
>>> [0:10] Tcl_EvalFile+0x134 [0xb9a8d4]
>>> [0:11] _ZN9ScriptTcl3runEPc+0x14 [0x9e5b82]
>>> [0:12] _Z18after_backend_initiPPc+0x22b [0x525053]
>>> [0:13] main+0x3a [0x524df2]
>>> [0:14] __libc_start_main+0xf4 [0x3dc541d994]
>>> [0:15] _ZNSt8ios_base4InitD1Ev+0x4a [0x5200fa]
>>>
>>>
>>> #################################
>>> custom Forcefield X-plor Format
>>> #################################
>>> REMARKS - parameter file ClayFF -
>>> REMARKS PARAMETER FROM ANDREY G. KALINICHEV ET AL JPCB 108:1255 (2004)
>>> REMARKS NO PARAMETERS FOR DIHEDRALS AND IMPROPERS
>>>
>>> set echo=false end
>>> !! - ALL PARAMETERS FROM ANDREY G.KALINICHEV ET AL JPCB 108:1255 (2004)
>>>
>>>
>>> bond o* h* 554.1349 1.0000 ! water
>>> bond oh ho 554.1349 1.0000 ! hydroxyl group
>>> bond ohs ho 554.1349 1.0000 ! hydroxyl substitution
>>> bond nh nh 220.8000 1.3940 ! amide group (N-N)
>>> bond nh hn 457.4590 1.0260 ! amide group (N-H)
>>>
>>> angle h* o* h* 45.7696 109.47 ! water
>>> angle nh nh hn 41.6000 110.00 ! amide (N-N-H)
>>> angle hn nh hn 38.0000 105.50 ! amide (H-N-H)
>>>
>>>
>>> {* Non Bonded Parameter section *}
>>> {* ============================ *}
>>> !!
>>> !
>>> ! atom eps sigma eps (1:4) sigma(1:4)
>>> ! type (kcal/mol) (A)
>>> ! --------------------------------------------------------------
>>> NONBonded h* 0.0000 0.0000 0.0000 0.0000
>>> NONBonded ho 0.0000 0.0000 0.0000 0.0000
>>> NONBonded o* 0.1554 3.1655 0.1554 3.1655
>>> NONBonded oh 0.1554 3.1655 0.1554 3.1655
>>> NONBonded ob 0.1554 3.1655 0.1554 3.1655
>>> NONBonded obos 0.1554 3.1655 0.1554 3.1655
>>>
>>> set echo=true end
>>>
>>> Sincerely
>>> Naresh
>>>
>>>
>>>
>>>> ----------------------------------------
>>>> From: johan strumpfer <johan.ks.uiuc_at_gmail.com>
>>>> Sent: Tue Jun 07 16:44:33 CEST 2011
>>>> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
>>>> Subject: Re: namd-l: water equilibration
>>>>
>>>>
>>>> Hi Naresh,
>>>>
>>>> As Bjoern said, your input script looks okay so to better diagnose it
>>>> we need more information. Could you rule out that it is not an error
>>>> with the custom force-field file and also post the contents of the log
>>>> file to give us more information.
>>>>
>>>> Cheers,
>>>> Johan
>>>>
>>>> ----------------------------------------------------------------
>>>> Johan Strumpfer (johanstr_at_ks.uiuc.edu)
>>>> Theoretical and Computational Biophysics Group
>>>> 3115 Beckman Institute
>>>> University of Illinois at Urbana-Champaign
>>>> 405 N. Mathews
>>>> Urbana, IL 61801, USA
>>>>
>>>>
>>>>
>>>> On Tue, Jun 7, 2011 at 10:03 AM, Narasimhan LOGANATHAN
>>>> <Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
>>>>> Hi,
>>>>> Yes. The custom force-field file is in X-plor format only and still
>> i have the
>>>>> errors.
>>>>>
>>>>> Sincerely,
>>>>> Naresh
>>>>>> ----------------------------------------
>>>>>> From: johan strumpfer <johanstr_at_ks.uiuc.edu>
>>>>>> Sent: Mon Jun 06 15:59:05 CEST 2011
>>>>>> To: Narasimhan LOGANATHAN <
>> Narasimhan.Loganathan_at_etu.univ-provence.fr>
>>>>>> Subject: Re: namd-l: water equilibration
>>>>>>
>>>>>>
>>>>>> Hi Naresh,
>>>>>>
>>>>>> You set paraTypeCharmm off, this would mean that your custom
>>>>>> force-field is in Xplor format - is this the case?
>>>>>>
>>>>>> Cheers,
>>>>>> Johan
>>>>>>
>>>>>>
>> ------------------------------------------------------------------------------------------------------
>>>>>> Johan Strumpfer: johanstr_at_ks.uiuc.edu
>> www.ks.uiuc.edu/~johanstr <http://www.ks.uiuc.edu/%7Ejohanstr>
>>>>>> Theoretical and Computational Biophysics Group
>>>>>> 3115 Beckman Institute
>>>>>> University of Illinois at Urbana-Champaign
>>>>>> 405 N. Mathews
>>>>>> Urbana, IL 61801, USA
>>>>>>
>> ------------------------------------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Jun 6, 2011 at 9:55 AM, Narasimhan LOGANATHAN
>>>>>> <Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> Yes. I copied all the error message. It didnt provide any other
>> information on the line which i went wrong.
>>>>>>>
>>>>>>> Sincerely
>>>>>>> Naresh
>>>>>>>> ----------------------------------------
>>>>>>>> From: Wang Yi <dexterwy_at_gmail.com>
>>>>>>>> Sent: Mon Jun 06 15:42:26 CEST 2011
>>>>>>>> To: Narasimhan LOGANATHAN <
>> Narasimhan.Loganathan_at_etu.univ-provence.fr>
>>>>>>>> Subject: Re: namd-l: water equilibration
>>>>>>>>
>>>>>>>>
>>>>>>>> Hey Naresh,
>>>>>>>>
>>>>>>>> Did you copy-and-paste all the error message? Usually in addition
>> to "FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE". NAMD should also tell
>> you the line at which the execution went into error. Do you have that?
>>>>>>>> ___________________________
>>>>>>>>
>>>>>>>> Yi (Yves) Wang
>>>>>>>> Duke University
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ? 2011-6-6???9:07? Narasimhan LOGANATHAN ???
>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>> I am a newbie to NAMD. Right now i am trying to equilibrate
>> water box.
>>>>>>>>> I am not using the CHARMM forcefield. Hence i defined my own
>> parameter file.
>>>>>>>>> However when i tried to equilibrate or minimize the water i am
>> getting the error
>>>>>>>>>
>>>>>>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>>>>>>>> Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>>>>>>>>
>>>>>>>>> Charm++ fatal error:
>>>>>>>>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Herewith, i have attached the config file. Could someone let me
>> know how can i proceed.
>>>>>>>>>
>>>>>>>>> structure water.psf
>>>>>>>>> coordinates water.pdb
>>>>>>>>>
>>>>>>>>> set temperature 300 ;# Tcl variable
>>>>>>>>> set outputname water-equi ;# Tcl variable
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> temperature $temperature ;# intialize velocities
>> randomly using Boltzmann Distribution
>>>>>>>>>
>>>>>>>>> firsttimestep 0
>>>>>>>>>
>>>>>>>>> ## Input and ForceField Parameters ##
>>>>>>>>> paratypeCharmm off
>>>>>>>>> parameters clayff-namd.inp
>>>>>>>>>
>>>>>>>>> if {0} {
>>>>>>>>> cellBasisVector1 31.212 0.0 0.0
>>>>>>>>> cellBasisVector2 0.0 27.000 0.0
>>>>>>>>> cellBasisVector3 0.0 0.0 30.000
>>>>>>>>> cellOrigin 0.0 0.0 0.0
>>>>>>>>> }
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ##exclude scaled1-4 ##
>>>>>>>>> ##1-4scaling 1.0 ##
>>>>>>>>> cutoff 12.0
>>>>>>>>> ##switching off ##
>>>>>>>>> ## swtichdist 10.0 ## to be used when switching is on
>> ##
>>>>>>>>> pairlistdist 14.0 ;# cutoff + 2 in general
>>>>>>>>> wrapAll on
>>>>>>>>>
>>>>>>>>> ## Integrator Parameters ##
>>>>>>>>>
>>>>>>>>> stepspercycle 2 ;# redefine pairlists every this
>> many timesteps
>>>>>>>>> timestep 1.0 ;# 1 fs/step
>>>>>>>>> rigidBonds all ;# to keep the water molecules
>> rigid
>>>>>>>>> nonbondedFreq 1 ;# no. of timesteps used to
>> calculate nonbonded interactions
>>>>>>>>> fullElectFrequency 1 ;# no. of timesteps used to
>> calculate electrostatic interactions
>>>>>>>>>
>>>>>>>>> ## Constant Temperature Control ##
>>>>>>>>> langevin on ;# Uses langevin dynamics for
>> controlling T (or) P
>>>>>>>>> langevinDamping 1.0 ;# Damping Coefficient in pico
>> seconds
>>>>>>>>> langevinTemp $temperature ;# random noise at this level
>>>>>>>>> langevinHydrogen no ;# no coupling of hydrogens
>>>>>>>>>
>>>>>>>>> ## Constant Pressure Control is done by the use of the
>> langevin dynamics (see manual) ##
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ## Particle Mesh Ewald ##
>>>>>>>>> PME yes
>>>>>>>>> PMEGridSpacing 1.0 ;# Alternatively we can specify
>> the PMEgrid Manually in case direction ##
>>>>>>>>>
>>>>>>>>>
>> #################################################################
>>>>>>>>> ### Output Options
>> ###
>>>>>>>>>
>> #################################################################
>>>>>>>>>
>>>>>>>>> outputname $outputname
>>>>>>>>> restartfreq 500
>>>>>>>>> dcdFreq 500
>>>>>>>>> xstFreq 200
>>>>>>>>> outputEnergies 100
>>>>>>>>> outputPressure 100
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>> ###################################################################
>>>>>>>>> ### IMD Settings
>> ###
>>>>>>>>>
>> ###################################################################
>>>>>>>>>
>>>>>>>>> if{0} {
>>>>>>>>> IMDon on
>>>>>>>>> IMDport 3000 ;# Enter this port number in VMD ##
>>>>>>>>> IMDfreq 1 ;# send every 1 frame ##
>>>>>>>>> IMDwait no ;# wait for VMD to connect before running
>> ##
>>>>>>>>> }
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>> ###################################################################
>>>>>>>>> ### Execution Script
>> ###
>>>>>>>>>
>> ###################################################################
>>>>>>>>> ## Minimization ##
>>>>>>>>> if {0} {
>>>>>>>>> minimize 100
>>>>>>>>> reinitvels $temperature
>>>>>>>>> }
>>>>>>>>>
>>>>>>>>> run 100000
>>>>>>>>>
>>>>>>>>> Thanks in advance
>>>>>>>>> Naresh
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>

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