Re: water equilibration

From: johan strumpfer (johan.ks.uiuc_at_gmail.com)
Date: Tue Jun 07 2011 - 11:20:16 CDT

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
>> >> 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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