Restart Annealing

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 30 2019 - 12:09:34 CDT

I have actually never had to restart the annealing step. I always have enough wall-time for MD. But, QMMM is quite slower, and so I need to restart my annealing step. I uncomment the binCoordinates, binVelocities, and extendedSystem, and type my .coor, .vel, and .xsc annealing file names here. Then I started the simulation again. But, it did not pick up with the last temperature and the temperature is going down every step, not up. What am I missing in my code to start from the last temperature and keep going to 300 K?:

cutoff 16
pairlistdist 18.0
switching on
switchdist 15
parameters toppar_all36_na_nad_ppi_gdp_gtp_qwikmd.str
############################################################################
#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-Ann.conf,v $
# $Author: jribeiro $ $Locker: $ $State: Exp $
# $Revision: 1.2 $ $Date: 2017/06/29 20:35:19 $
#
############################################################################
##START HERE###
##Simulation Template##
# Simulation conditions
coordinates Simulation_QwikMD.pdb
structure Simulation_QwikMD.psf

binCoordinates QMMM-Ann.restart.coor
binVelocitiesQMMM-Ann.restart.vel
extendedSystem QMMM-Ann.restart.xsc

# Simulation conditions
#temperature 60

# Harmonic constraints

constraints on
consref QMMM-Min_restraints.pdb
conskfile QMMM-Min_restraints.pdb
constraintScaling 2
consexp 2
conskcol B

# Output Parameters

binaryoutput no
outputname QMMM-Ann2
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile QMMM-Ann2.dcd
dcdfreq 1
XSTFreq 1
restartfreq 1
restartname QMMM-Ann2.restart

# Thermostat Parameters
langevin on
langevintemp 60
langevinHydrogen on
langevindamping 50

# Barostat Parameters

usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston off
langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 60

# 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 cu_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 Simulation_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-Ann"

# 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

# With Live Solvent Selection, NAMD will automatically keep track of the
# solvent molecules for all QM Groups, and will exchange classical solvent
# molecules with QM solvent molecules every "QMLSSFreq" steps.

QMLiveSolventSel on

# 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 "!RI BP86 def2-SVP def2/J Grid5 NoFinalGrid EnGrad NormalSCF"
qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"
qmConfigLine "%%output Print\[ P_Basis \] 2 Print\[ P_MOs \] 1 end"
qmConfigLine %%scf
qmConfigLine maxiter 2000
qmConfigLine shift shift 0.1 erroff 0 end
qmConfigLine damp fac 0.80 erroff 0.0001 end
qmConfigLine end
qmConfigLine "%%pal nprocs 16 end"

# Multiplicity of the QM region.

qmMult 1 2

# Indicates the charge of each QM region.

qmCharge 1 2.00

# Indicates which QM software should be used.

qmSoftware ORCA

# Path to the executable

qmExecPath "/zhome/kmcguir/.local/orca_4_1_1_linux_x86-64_openmpi313/orca"

# 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
set Temp 300
set barostat 0
set nSteps 3
for {set t 60} {$t <= $Temp} {incr t} {run $nSteps;langevintemp $t;if {$barostat} {langevinpistontemp $t}}

set file [open QMMM-Ann.check w+]
set done 1
if {[file exists QMMM-Ann.restart.coor] != 1 || [file exists QMMM-Ann.restart.vel] != 1 || [file exists QMMM-Ann.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
}

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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