From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Thu Sep 30 2021 - 11:15:00 CDT
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:
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
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
#PME(for full-system periodic electrostatics)
#Constant Temperature Control
#langevin on ;# do langevin dynamics
#langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
#Constant Pressure Control (variable volume)
useGroupPressure no ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
run5000000 ;#10 ns
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