Re: water equilibration

From: Gurunath Katagi (gurukatagi_at_gmail.com)
Date: Tue Jun 07 2011 - 15:14:51 CDT

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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