From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Thu Sep 30 2021 - 16:40:12 CDT
As you said, with PME set to off, Ihave got the same simulation speed for both box sizes. That helped a lot. Thankyou so much.
On Thursday, September 30, 2021, 10:27:05 PM GMT+3:30, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
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Hi Fateme,
The performance variation is almost assuredly PME’s fault, since PME decomposes the system into grids to calculate long-range electrostatics. There are 1000x more grid elements in a cube of side length 500 Angstroms relative to one with 50 Angstroms. I’m betting if you turned PME off, the simulation performance for your NVE systems would be identical regardless of the box dimension.
-Josh
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Fateme Ghadirian <fateme.ghadirian_at_REMOVE_yahoo.com>
Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, Fateme Ghadirian <fateme.ghadirian_at_yahoo.com>
Date: Thursday, September 30, 2021 at 12:40 PM
To: NAMD List <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Simulation Box Size & Simulation speed
Dear NAMD users,
I have a system which contains one particle (HO) in vacuum. I am trying to simulate a gaseous system, it is a part of Heat of vaporization’s calculation.
Langevin is set to off, due to lack of one particle’s ability to maintain system’s temperature. Run is in NVT.
As the system 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 hours needed to complete the simulation).
When I decrease the size of the simulation box to 50 Ang in each direction, the simulation speed increases (0.0016 days/ns~ 0.4 hour to complete the simulation).
As I understood simulation speed can just be affected with number of particles, due to the number of equations of motion which would be calculated. So how simulation box size can affect simulation speed in this case?
Here is my Configuration file:
structure x.psf
coordinates x.pdb
set new_run run-0
outputName ./$new_run/$new_run
set temperature 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
}
run 5000000 ;#10 ns
Thanks in advance
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