How to avoid producing a huge DCD file?

From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Mon Mar 23 2020 - 22:15:53 CDT

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
}

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