Equilibration simulation too slow.

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Sun Dec 07 2008 - 09:59:35 CST

Hello,
I am running an equilibration simulation for a protein (fascin) in a water
box on a linux-amd64 cluster with Rocks OS. I had some trouble with it
before, but I got to run with the help of people in the NAMD community, but
to do so I had to increase parameters such as margin (10), cutoff (15),
pairlistdist (25), and langevinPistonPeriod while reducing the timestep (0.5
fs).

In this simulation I gradually raise the temperature by 10K every 500 steps
until it reaches 310K, starting at 1K. In the first steps it starts very
slow (~4s/step), but quickly levels off at ~0.7s/step. I know these exact
numbers are irrelevant, but I have been told such a simulation should run
faster.

Does anybody have any suggestions on what other parameter could be altered
to improve the efficiency? I am copying my configuration file below. Thank
you for your attention.

Diego A. Vargas
________________________________________________________________

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure /wt_fascin_wb.psf
coordinates /wt_fascin_wb.pdb
bincoordinates /wt_fascin_wb_mn.restart.coor

binvelocities /wt_fascin_wb_mn.restart.vel

extendedSystem /wt_fascin_wb_mn.restart.xsc

set temperature 310
set outputname ***

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp

# Force-Field Parameters

exclude scaled1-4
1-4scaling 1.0
cutoff 12.

switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 0.5

rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

margin 50.0

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 1
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
# extendedSystem used.

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 100
PMEGridSizeY 128
PMEGridSizeZ 100

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 400.
langevinPistonDecay 200.
langevinPistonTemp 1

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Gradual temperature increase:
run 500
for {set i 10} {$i <= $temperature} {incr i 10} {
langevinTemp $i
langevinPistonTemp $i
run 500
}
run 1000000 ;# 500ps

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