Re: Simulation Box Size & Simulation speed

From: Fateme Ghadirian (
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 <> wrote:
 <!--#yiv2079955588 _filtered {} _filtered {} _filtered {}#yiv2079955588 #yiv2079955588 p.yiv2079955588MsoNormal, #yiv2079955588 li.yiv2079955588MsoNormal, #yiv2079955588 div.yiv2079955588MsoNormal {margin:0in;font-size:11.0pt;font-family:"Calibri", sans-serif;}#yiv2079955588 p.yiv2079955588ydp1d16584msonormal, #yiv2079955588 li.yiv2079955588ydp1d16584msonormal, #yiv2079955588 div.yiv2079955588ydp1d16584msonormal {margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:"Calibri", sans-serif;}#yiv2079955588 span.yiv2079955588EmailStyle19 {font-family:"Calibri", sans-serif;color:windowtext;}#yiv2079955588 .yiv2079955588MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv2079955588 div.yiv2079955588WordSection1 {}-->
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.
From: <> on behalf of Fateme Ghadirian <>
Reply-To: "" <>, Fateme Ghadirian <>
Date: Thursday, September 30, 2021 at 12:40 PM
To: NAMD List <>
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

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST