(no subject)

From: ΠμΦΣΊΣ (zhhxu_at_mail.ipe.ac.cn)
Date: Mon Jan 02 2012 - 03:03:31 CST

Hi NAMD-Users
I have test 10 ns CG-MD simulation of membrane system containing 1169 popc_lipids and 43181 CG-waters(61540 CG-atoms in sum)on a computer with 8 cpucores and 4 GPUs, the conf file is attached below.The benchmark time 0.2364 s/step appear to be slower as compared with a all-atom simulation(a containing 274 popc and 18350 water and in sum 91766 atoms, the benchmark time is 0.05s/step).What is reason for this ? could you give me a sample conf file of coarse grain simulation? Thanks in advance for any suggestions.
 
With best regards
 
zhonghe
graduate student
IPE,CAS.
##########
parameters input/rbcg-2007.par
exclude 1-2
cutoff 12.0
switching on
switchdist 9.0
pairlistdist 16.0
dielectric 20.0
hgroupcutoff 0
margin 4
# Integrator Parameters
timestep 20.0
nonbondedFreq 1
stepspercycle 10
wrapAll on
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 250
PMEGridSizeY 250
PMEGridSizeZ 135
# Constant Temperature Control
langevin on
langevinDamping 5.0
langevinTemp 300
langevinHydrogen off
# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell yes
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp 300
# Minimization
minimize 2000
reinitvels 300
 run 500000 ;# 10ns
###########

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