Re: water equilibration

From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Thu Aug 04 2011 - 03:25:07 CDT

Hi,
Thanks for the reply. I was kept busy on some other task.
I changed all the things u mentioned and i tried to run it.
I got an error message "splitPatch hydrogen".

However i have added the splitPatch hydrogen in my config file.
Still i receive the error.Could you kindly help to overcome this.

Herewith i send you the config file.

#######################################################
## Simulation of Bulk Water ##
#######################################################

## Minimization and Equilibration of Water Box ##

#######################################################
## Adjustable Parameters ##
#######################################################

structure water.psf
coordinates water.pdb

set temperature 300 ;# Tcl variable
set outputname water-equi ;# Tcl variable

## starting from scratch ##

temperature $temperature ;# intialize velocities randomly using
Boltzmann Distribution

firsttimestep 0

#######################################################
## Simulation Parameters ##
#######################################################

## Input and ForceField Parameters ##
paratypeCharmm off
parameters clayff-namd-1.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 none
## 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 10 ;# redefine pairlists every this many timesteps
timestep 1.0 ;# 1 fs/step
rigidBonds water ;# 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
splitPatch hydrogen

## Constant Temperature Control ##
langevin on ;# Uses langevin dynamics for controlling T
(or) P
langevinDamping 2 ;# 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
Naresh

> ----------------------------------------
> From: johan strumpfer <johan.ks.uiuc_at_gmail.com>
> Sent: Tue Jun 07 18:20:16 CEST 2011
> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> Subject: Re: namd-l: water equilibration
>
>
> 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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