From: Julio Maia (jmaia_at_ks.uiuc.edu)
Date: Tue Mar 24 2020 - 00:09:00 CDT
If you avoid doing I/O every time step, that will certainly decrease the
size of your trajectory file.
Bump the following keywords
*dcdfreq 1 XSTFreq 1 restartfreq 1*
to a higher value and see if that helps.
Best,
On Mon, Mar 23, 2020 at 11:59 PM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
> How to avoid producing a huge DCD file?
>
> A huge QMMM.dcd output file with a 52G size has been produced and the
> linux system warned the disk is full when I run a QM/MM molecule dynamic
> for an enzyme over one night by QWIKMD, I do not know how to modfiy config
> file and to avoid producing the huge DCD file?
>
> Any suggesion will be much appreciate, thank you for your help in advanced
>
> The conf file is as follows:
>
> cutoff 12.0
> pairlistdist 14.0
> switching on
> switchdist 10.0
> PME on
> PMEGridspacing 1
> wrapAll on
> wrapWater on
> # IMD Parameters
> IMDon on ;#
> IMDport 3000 ;# port number (enter it in VMD)
> IMDfreq 10 ;# send every 10 frame
> IMDwait yes ;# wait for VMD to connect before running?
> IMDignoreForces yes ;#monitor without the possibility of perturbing the
> simulation
>
>
> ############################################################################
> #cr
> #cr (C) Copyright 1995-2009 The Board of Trustees of the
> #cr University of Illinois
> #cr All Rights Reserved
> #cr
>
> ############################################################################
>
>
> ############################################################################
> # RCS INFORMATION:
> #
> # $RCSfile: QMMM.conf,v $
> # $Author: jribeiro $ $Locker: $ $State: Exp $
> # $Revision: 1.2 $ $Date: 2017/06/29 20:35:19 $
> #
>
> ############################################################################
> ##START HERE###
> ##Simulation Template##
> # Simulation conditions
> coordinates NF216-QM_QwikMD.pdb
> structure NF216-QM_QwikMD.psf
>
> binCoordinates QMMM-Equi.restart.coor
> binVelocities QMMM-Equi.restart.vel
> extendedSystem QMMM-Equi.restart.xsc
>
> # Simulation conditions
> #temperature 0
>
>
> # Harmonic constraints
>
> constraints off
> consref qwikmdTemp_constraints.pdb
> conskfile qwikmdTemp_constraints.pdb
> constraintScaling 2
> consexp 2
> conskcol B
>
>
> # Output Parameters
>
> binaryoutput no
> outputname QMMM
> outputenergies 1
> outputtiming 1
> outputpressure 1
> binaryrestart yes
> dcdfile QMMM.dcd
> dcdfreq 1
> XSTFreq 1
> restartfreq 1
> restartname QMMM.restart
>
> # mobile atom selection:
> # protein-mm
>
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile proteinfixed.pdb
> fixedAtomsCol B
>
>
> # Thermostat Parameters
> langevin on
> langevintemp 300
> langevinHydrogen on
> langevindamping 50
>
> # Barostat Parameters
>
> usegrouppressure yes
> useflexiblecell no
> useConstantArea no
> langevinpiston on
> langevinpistontarget 1.01325
> langevinpistonperiod 200
> langevinpistondecay 100
> langevinpistontemp 300
>
> # Integrator Parameters
>
> timestep 0.5
> firstTimestep 0
> fullElectFrequency 1
> nonbondedfreq 1
> stepspercycle 1
>
> # Force Field Parameters
>
> paratypecharmm on
> parameters toppar_water_ions_namd.str
> parameters toppar_all36_carb_glycopeptide.str
> parameters par_all36_lipid.prm
> parameters par_all36_na.prm
> parameters par_all36_prot.prm
> parameters par_all36_carb.prm
> parameters par_all36_cgenff.prm
> parameters MFA_qwikmd.str
> exclude scaled1-4
> 1-4scaling 1.0
> rigidbonds none
>
>
> #Implicit Solvent Parameters
>
> gbis off
> alphaCutoff 14.0
> ionConcentration 0.15
>
> # Truns ON or OFF the QM calculations
>
> qmForces on
>
> #printExclusions on
>
> # Name of a secondary PDB file where the OCCupancy
> # or BETA column has the indications for QM or MM atoms.
>
> qmParamPDB NF216-QM_QwikMD_qm-input.pdb
>
> # Indicates qhich column has the QM/MM field.
>
> qmColumn beta
>
> # Number of simultaneous QM simulations per node
>
> QMSimsPerNode 1
>
> # Indicates qhich column has the QM-MM bond information.
>
> qmBondColumn occ
>
> # Indicates wether the value in the BondColumn will define the distance
> # between the QM atom and the Dummy atom that will replace the MM atom
>
> # qmBondDist on
>
> # Indicates if the values in the bond column represent either:
> # LEN: the length betwen the QM and dummy atoms.
>
> # QMBondValueType len
>
> # User defined Link Atom element.
>
> #QMLinkElement "18 38 Cl"
>
> # Indicates what will be the treatment given to QM-MM bonds in terms of
> # charge distribution and dummy atom creation and placement.
>
> QMBondScheme CS
>
> # This will scale down the point charges representing the classical system
> # as to replicate the switching procedure that NAMD applies to all charged
> # interaction.
>
> QMSwitching on
>
> # This option is used to decide which kind of function will be used to
> scale
> # down point charges sent to QM calculations.
>
> QMSwitchingType Switch
>
> # This will alter the point charges presented to the QM system.
>
> QMPointChargeScheme Round
>
> # Directory where QM calculations will be ran.
>
> qmBaseDir "[pwd]/qmmm_exec/QMMM"
>
> # Indicates to NAMD that ALL forces form NAMD will be ignored and only
> # the gradients from the QM software will be applied on the atoms.
>
> qmReplaceAll OFF
>
> # The QM code will change all QM atom's VdW types to "q"+element for VdW
> interactions.
>
> QMVdWParams off
>
> # Indicates that no Poitn Charges should be selected and applied in
> # QM systems.
>
> qmElecEmbed On
>
> # Sets a stride for new point charge determination.
>
> QMPCStride 1
>
> # Indicates that one or more files will be provided with a custom selection
> # of point charges.
>
> QMCustomPCSelection off
>
> # The file will have, in the "qmColumn", the same QM ID provided for a
> single QM group.
>
> QMCustomPCFile input-CustomPC-1.0.pdb
>
>
> QMLiveSolventSel off
>
> # This indicate which residue type will be used in LSS.
>
> QMLSSResname TIP3
>
> # Frequency of LSS.
>
> QMLSSFreq 50
>
> # For LSS, this indicates how solvent molecules are selected.
>
> QMLSSMode dist
>
>
> # This will indicate which residues are to be used in the determination of
> the
> # COM of non-solvent QM atoms.
>
> QMLSSRef "1 RP1 9"
>
> # The string passed to "qmConfigLine" will be copied and pasted at the very
> # begining of the configuration file for the chosen QM software.
>
> qmConfigLine "PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK"
> qmConfigLine "Test System"
>
> # Multiplicity of the QM region.
>
> qmMult 1 1
>
> # Indicates the charge of each QM region.
>
> qmCharge 1 1.00
>
>
> # Indicates which QM software should be used.
>
> qmSoftware MOPAC
>
> # Path to the executable
>
> qmExecPath "/opt/mopac/MOPAC2016.exe"
>
> # Charge mode expected from the QM software.
>
> QMChargeMode mulliken
>
> # Frequency of QM charge output.
>
> QMOutStride 1
>
> # Frequency of QM ONLY position output.
>
> QMPositionOutStride 1
>
> # Number of steps in the QM/MM simulation
>
> # Script
> run 500000
>
> set file [open QMMM.check w+]
> set done 1
> if {[file exists QMMM.restart.coor] != 1 || [file exists QMMM.restart.vel]
> != 1 || [file exists QMMM.restart.xsc] != 1 } {
> set done 0
> }
> if {$done == 1} {
> puts $file "DONE"
> flush $file
> close $file
> } else {
> puts $file "One or more files failed to be written"
> flush $file
> close $file
> }
>
>
-- *JULIO MAIA* *Research Programmer* Beckman Institute for Advanced Science and Technology Vice Chancellor Research Institutes University of Illinois at Urbana-Champaign 405 N. Mathews Avenue | M/C 251 Urbana, IL 61801 217-244-1928 | jmaia_at_ks.uiuc.edu beckman.illinois.edu <http://illinois.edu/> *Under the Illinois Freedom of Information Act any written communication to or from university employees regarding university business is a public record and may be subject to public disclosure. *
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