Temperature Fluctuations in Drude Simulations - NAMD

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Thu Oct 04 2018 - 23:39:14 CDT

Hi,

I'm trying to perform an NVT simulation with Drude polarizable model. I
find that that Temperature fluctuates around 470 K, when I have set the
temperature to be 298K. I have attached my Input file below, any help in
this regard would be much appreciated.

The system is a solvated system of graphene sheet and DNA bases.

structure test.psf
coordinates __final.pdb

set temp 300;
set outputname step3_mini;

temperature $temp;
outputName $outputname; # base name for output from this run
                                # NAMD writes two files at the end, final
coord and vel
                                # in the format of first-dyn.coor and
first-dyn.vel
firsttimestep 0; # last step of previous run
restartfreq 500; # 500 steps = every 1ps
dcdfreq 1000;
dcdUnitCell yes; # the file will contain unit cell
info in the style of
                                       # charmm dcd files. if yes, the dcd
files will contain
                                       # unit cell information in the style
of charmm DCD files.
xstFreq 1000; # XSTFreq: control how often the
extended systen configuration
                                       # will be appended to the XST file
outputEnergies 125; # 125 steps = every 0.25ps
                                       # The number of timesteps between
each energy output of NAMD
outputTiming 1000; # The number of timesteps between
each timing output shows
                                       # time per step and time to
completion

# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type parameter
file(s)
                                       # multiple definitions may be used
but only one file per definition

parameters ../toppar_drude/toppar_drude_master_protein_2013e.str;
parameters ../toppar_drude/toppar_drude_lipid_2017b.str;
parameters ../toppar_drude/toppar_drude_model_2013e.str;
parameters ../toppar_drude/toppar_drude_carbohydrate_2013e.str;
parameters ../toppar_drude/toppar_drude_nucleic_acid_2017b.str;

# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to use
"none,1-2,1-3,1-4,or scaled1-4"
                                       # 1-2: all atoms pairs that are
bonded are going to be ignored
                                       # 1-3: 3 consecutively bonded are
excluded
                                       # scaled1-4: include all the 1-3,
and modified 1-4 interactions
                                       # electrostatic scaled by 1-4scaling
factor 1.0
                                       # vdW special 1-4 parameters in
charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching no; # force-based switching of vdW
should not be used for Drude FF
mergeCrossterms on

# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with
PME
switchdist 10.0; # cutoff - 2.
                                       # switchdist - where you start to
switch
                                       # cutoff - where you stop accounting
for nonbond interactions.
                                       # correspondence in charmm:
                                       # (cutnb,ctofnb,ctonnb =
pairlistdist,cutoff,switchdist)
pairlistdist 14.0; # stores the all the pairs with in
the distance it should be larger
                                       # than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
                                       # cycle represents the number of
steps between atom reassignments
                                       # this means every 20/2=10 steps the
pairlist will be updated

# Integrator Parameters
timestep 0.1; # fs/step
rigidBonds all; # Bound constraint all bonds
involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step

# Use Drude polarizable model
drude on
drudeTemp 1
drudeHardwall on
drudeDamping 20.0
drudeBondLen 0.2
drudeBondConst 40000
drudeNbtholeCut 5.0

# Langevin Dynamics
langevin on; # do langevin dynamics
langevinDamping 1; # damping coefficient (gamma) of
1/ps
langevinTemp $temp; # bath temperature
langevinHydrogen no; # don't couple langevin bath to
hydrogens
seed 12345

# mobile atom selection:
# resname ADEB SWM4
fixedAtoms on
fixedAtomsFile Minimization_fixed.pdb
fixedAtomsCol O

# PBC
cellBasisVector1 51.766 0.00 0.00
cellBasisVector2 0.00 29.424 0.00
cellBasisVector3 0.00 0.00 16.572
cellOrigin -0.403 -0.082 6.472
wrapAll on

PME yes
PMEGridSizeX 50
PMEGridSizeY 30
PMEGridSizeZ 16

minimize 200000
run 20000

-- 
*Hemanth H 18310019*
Research Scholar
IIT Gandhinagar

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