PME or not PME? What happens if PME is turned off?

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Jul 18 2011 - 04:10:08 CDT

Hi,

I just happened to run a simulation with PME turned off.
I realized this after the first run and rerun the simulation with PME turned
on.

Interestingly the simulation without PME was faster so I am wondering if full
electrostatics are still calculated without PME and which algorithm is used.
If this is true, at which estimate system size is PME faster?

PME OFF:
Benchmark time: 48 CPUs 0.0764298 s/step 0.442302 days/ns 166.52 MB memory
Benchmark time: 48 CPUs 0.0758653 s/step 0.439035 days/ns 166.52 MB memory
Benchmark time: 48 CPUs 0.0765887 s/step 0.443222 days/ns 166.52 MB memory

PME ON:
Benchmark time: 48 CPUs 0.08812 s/step 0.509954 days/ns 167.578 MB memory
Benchmark time: 48 CPUs 0.0879751 s/step 0.509115 days/ns 167.578 MB memory
Benchmark time: 48 CPUs 0.0879445 s/step 0.508938 days/ns 167.578 MB memory

Does the parameter "fullElectFrequency" only apply when PME is activated?
It is not referenced in the output file. Neither as "set but unused variable"
nor as "Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1" as when PME is
turned on.

To sum it up:
If my system is smaller then XYZ, am I better of without PME?

*confused*

Some info about the system:

Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 11500000
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 98 0 0
Info: PERIODIC CELL BASIS 2 0 98 0
Info: PERIODIC CELL BASIS 3 0 0 89.8903
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: SWITCHING ACTIVE
Info: SWITCHING ON 15
Info: SWITCHING OFF 16
Info: PAIRLIST DISTANCE 17
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 1.17
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 20.67
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 294.15
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 294.15 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS -6.49826e-05 3.88208e-05 -1.83779e-05
Info: CELL FLUCTUATION IS ANISOTROPIC
Info: CONSTANT AREA PRESSURE CONTROL ACTIVE
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1310977009
Info: USE HYDROGEN BONDS? NO
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_lipid.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 119 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 89020 ATOMS
Info: 60063 BONDS
Info: 33286 ANGLES
Info: 6546 DIHEDRALS
Info: 404 IMPROPERS
Info: 148 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 87663 RIGID BONDS
Info: 179397 DEGREES OF FREEDOM
Info: 30162 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 30162 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 540702 amu
Info: TOTAL CHARGE = 1.99676e-06 e
Info: MASS DENSITY = 1.04005 g/cm^3
Info: ATOM DENSITY = 0.103115 atoms/A^3
Info: *****************************

Cheers,
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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