From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Thu Sep 30 2021 - 11:15:00 CDT
DearNAMD users,
Ihave a system which contains one particle (HO) in vacuum. I am trying to simulatea gaseous system, it is a part of Heat of vaporization’s calculation.
Langevinis set to off, due to lack of one particle’s ability to maintain system’stemperature. Run is in NVT.
As thesystem is trying to represent a gaseous system, simulation box size is large;500 Ang in each Direction (Simulation speed is 0.072 days/ns, so ~ 17 hoursneeded to complete the simulation).
WhenI decrease the size of the simulation box to 50 Ang in each direction, thesimulation speed increases (0.0016 days/ns~ 0.4 hour to complete the simulation).
As Iunderstood simulation speed can just be affected with number of particles, dueto the number of equations of motion which would be calculated. So how simulationbox size can affect simulation speed in this case?
Hereis my Configuration file:
structurex.psf
coordinatesx.pdb
setnew_run run-0
outputName./$new_run/$new_run
settemperature 123.
firsttimestep 0
paraTypeCharmm on
parameters ./param/par_all36_lipid.prm
temperature $temperature
if{1} {
cellBasisVector1 500.0 0.0 0.0
cellBasisVector2 0.0 500.0 0.0
cellBasisVector3 0.0 0.0 500.0
cellOrigin 0.0 0.0 0.0
}
wrapAll on
#Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
#Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME(for full-system periodic electrostatics)
if{1} {
PME yes
PMEGridSpacing 1.0
}
#Constant Temperature Control
#langevin on ;# do langevin dynamics
#langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
#langevinTemp $temperature
#Constant Pressure Control (variable volume)
if{0} {
useGroupPressure no ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
restartfreq 100
dcdfreq 5000
xstFreq 100
outputEnergies 100
outputPressure 100
#Minimization 5ps
if{1} {
minimize 10
reinitvels $temperature
}
run5000000 ;#10 ns
Thanksin advance
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST