Re: Restart Annealing

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 30 2019 - 13:48:45 CDT

I think I found the problem. I left firsttimestep as zero instead of looking at the restart.xsc file and getting the last step and setting that to firsttimestep.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Saturday, March 30, 2019 11:09 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Restart Annealing

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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