Hello,

I am using NAMD for simulation at 100 ns. I am having laptop specifications Windows 10, 1TB hard disc, 8gb ram, AMD processor, 4gb NVIDIA graphics card.

I ran the simulation for 0.25 ns just to check how it runs and it ran just in 10 minutes. But when I ran it for 100ns, it is taking lot of time (more than a 12 hours).

Here, I am attaching my config file. please anyone tell me what mistakes I am doing.

structure step3_input.psf

coordinates step3_input.pdb

set temp 303.15;

set outputname step4_equilibration;

# read system values written by CHARMM (need to convert uppercases to lowercases)

#exec tr "\[:upper:\]" "\[:lower:\]" < ../step3_pbcsetup.str | sed -e "s/ =//g" > step3_input.str

#source step3_input.str

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 10000; # 500 steps = every 1ps

dcdfreq 100000;

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 5000; # XSTFreq: control how often the extended systen configuration

# will be appended to the XST file

outputEnergies 100000; # 125 steps = every 0.25ps

# The number of timesteps between each energy output of NAMD

outputTiming 10000; # 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/par_all36m_prot.prm

parameters toppar/par_all36_na.prm

parameters toppar/par_all36_carb.prm

parameters toppar/par_all36_lipid.prm

parameters toppar/par_all36_cgenff.prm

parameters toppar/par_interface.prm

parameters toppar/toppar_all36_moreions.str

parameters toppar/toppar_all36_nano_lig.str

parameters toppar/toppar_all36_nanolig_patch.str

parameters toppar/toppar_all36_synthetic_polymer.str

parameters toppar/toppar_all36_synthetic_polymer_patch.str

parameters toppar/toppar_all36_polymer_solvent.str

parameters toppar/toppar_water_ions.str

parameters toppar/toppar_dum_noble_gases.str

parameters toppar/toppar_ions_won.str

parameters toppar/toppar_all36_prot_arg0.str

parameters toppar/toppar_all36_prot_c36m_d_aminoacids.str

parameters toppar/toppar_all36_prot_fluoro_alkanes.str

parameters toppar/toppar_all36_prot_heme.str

parameters toppar/toppar_all36_prot_na_combined.str

parameters toppar/toppar_all36_prot_retinol.str

parameters toppar/toppar_all36_prot_modify_res.str

parameters toppar/toppar_all36_na_nad_ppi.str

parameters toppar/toppar_all36_na_rna_modified.str

parameters toppar/toppar_all36_lipid_archaeal.str

parameters toppar/toppar_all36_lipid_bacterial.str

parameters toppar/toppar_all36_lipid_cardiolipin.str

parameters toppar/toppar_all36_lipid_cholesterol.str

parameters toppar/toppar_all36_lipid_dag.str

parameters toppar/toppar_all36_lipid_inositol.str

parameters toppar/toppar_all36_lipid_lnp.str

parameters toppar/toppar_all36_lipid_lps.str

parameters toppar/toppar_all36_lipid_mycobacterial.str

parameters toppar/toppar_all36_lipid_miscellaneous.str

parameters toppar/toppar_all36_lipid_model.str

parameters toppar/toppar_all36_lipid_prot.str

parameters toppar/toppar_all36_lipid_sphingo.str

parameters toppar/toppar_all36_lipid_tag.str

parameters toppar/toppar_all36_lipid_yeast.str

parameters toppar/toppar_all36_lipid_hmmm.str

parameters toppar/toppar_all36_lipid_detergent.str

parameters toppar/toppar_all36_lipid_ether.str

parameters toppar/toppar_all36_carb_glycolipid.str

parameters toppar/toppar_all36_carb_glycopeptide.str

parameters toppar/toppar_all36_carb_imlab.str

parameters toppar/toppar_all36_label_spin.str

parameters toppar/toppar_all36_label_fluorophore.str

parameters ../unl/unl.prm # Custom topology and parameter files for UNL

# 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 on; # New option for force-based switching of vdW

# if both switching and vdwForceSwitching are on CHARMM force

# switching is used for vdW forces.

# You have some freedom choosing the cutoff

cutoff 20.0; # 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 22.0; # 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 1.0; # 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

# Constant Temperature Control ONLY DURING EQUILB

reassignFreq 100000 # reassignFreq: use this to reassign velocity every 500 steps

reassignTemp $temp;

# Periodic Boundary conditions. Need this since for a start...

cellBasisVector1 83.59 0.0 0.0; # vector to the next image

cellBasisVector2 0.0 83.90 0.0;

cellBasisVector3 0.0 0.0 83.82;

cellOrigin 0.011 0.074 0.018; # the *center* of the cell

wrapWater on; # wrap water to central cell

wrapAll on; # wrap other molecules too

wrapNearest off; # use for non-rectangular cells (wrap to the nearest image)

# PME (for full-system periodic electrostatics)

PME yes;

PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)

PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size

# Constant Temperature Control

langevin on

langevinDamping 1.0

langevinTemp $temp

langevinHydrogen off

constraints on

consexp 2

consref restraints/prot_posres.ref

conskfile restraints/prot_posres.ref

conskcol B

constraintScaling 1.0

minimize 100000

numsteps 50000000

run 50000000