[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

Jiaqi Lin jqlin at mit.edu
Thu Jan 15 03:22:32 CET 2015

Dear GMX developers,

I've encounter a problem in GROMACS concerning the auto-tuning feature 
of PME that bugged me for months. As stated in the title, the 
auto-tuning feature of mdrun changed my coulomb cutoff from 1.4 nm to 
~3.3 nm (stated in md.log) when I set -npme to be 28 (128 total CPU 
cores), and this giving me interesting simulation results. When I use 
-notunepme, I found Coulomb (SR) and recip. giving me same energy but 
the actual simulation result is different. This i can understand: 
scaling between coulombic cut-off/grid size theoretically give same 
accuracy to electrostatics (according to GMX manual and PME papers), but 
there actually some numerical error due to grid mapping and even if the 
energy is the same that does not mean system configuration has to be the 
same (NVE ensemble: constant energy, different configuration).
However the thing i don't understand is the following. I am interested 
in the result under large coulomb cut-off, so I try to manually set 
cut-off and grid space with -notunepme, using the value tuned by mdrun 
previously. This give me complete different simulation result, and the 
energy is also different. I've tried to set rlist, rlistlong, or both to 
equal rcoulomb (~3.3) still does not give me the result produced by 
auto-tuning PME. In addition, simulation speed dramatically reduces when 
I set rcoulomb to be ~3.3 (using -tunepme the speed remains nearly the 
same no matter how large the cutoff is tuned to). I've tested this in 
both GMX 4.6.5 and 5.0.1, same thing happens, so clearly it's not 
because of versions. Thus the question is: what exactly happened to PME 
calcualtion using the auto-tuning feature in mdrun, why it does give 
different results when I manually set the coulomb cutoff and grid space 
to the value tuned by mdrun without the auto-tuning feature (using 
-notunepme)? Thank you for help.

additional info: I use Group cutoff-scheme , rvdw is  1.2.

  md.log file:
DD  step 9 load imb.: force 29.4%  pme mesh/force 3.627

step   30: timed with pme grid 280 280 384, coulomb cutoff 1.400: 1026.4 
step   50: timed with pme grid 256 256 324, coulomb cutoff 1.464: 850.3 
step   70: timed with pme grid 224 224 300, coulomb cutoff 1.626: 603.6 
step   90: timed with pme grid 200 200 280, coulomb cutoff 1.822: 555.2 
step  110: timed with pme grid 160 160 208, coulomb cutoff 2.280: 397.0 
step  130: timed with pme grid 144 144 192, coulomb cutoff 2.530: 376.0 
step  150: timed with pme grid 128 128 160, coulomb cutoff 2.964: 343.7 
step  170: timed with pme grid 112 112 144, coulomb cutoff 3.294: 334.8 
Grid: 12 x 14 x 14 cells
step  190: timed with pme grid 84 84 108, coulomb cutoff 4.392: 346.2 
step  190: the PME grid restriction limits the PME load balancing to a 
coulomb cut-off of 4.392
step  210: timed with pme grid 128 128 192, coulomb cutoff 2.846: 360.6 
step  230: timed with pme grid 128 128 160, coulomb cutoff 2.964: 343.6 
step  250: timed with pme grid 120 120 160, coulomb cutoff 3.036: 340.4 
step  270: timed with pme grid 112 112 160, coulomb cutoff 3.253: 334.3 
step  290: timed with pme grid 112 112 144, coulomb cutoff 3.294: 334.7 
step  310: timed with pme grid 84 84 108, coulomb cutoff 4.392: 348.0 
               optimal pme grid 112 112 160, coulomb cutoff 3.253
DD  step 999 load imb.: force 18.4%  pme mesh/force 0.918

At step 1000 the performance loss due to force load imbalance is 6.3 %

NOTE: Turning on dynamic load balancing

            Step           Time         Lambda
            1000       20.00000        0.00000

    Energies (kJ/mol)
            Bond       G96Angle        LJ (SR)   Coulomb (SR)   Coul. recip.
     1.98359e+05    1.79181e+06   -1.08927e+07   -7.04736e+06 -2.32682e+05
  Position Rest.      Potential    Kinetic En.   Total Energy Temperature
     6.20627e+04   -1.61205e+07    4.34624e+06   -1.17743e+07 3.00659e+02
  Pressure (bar)   Constr. rmsd
     2.13582e+00    1.74243e-04


Jiaqi Lin
postdoc fellow
The Langer Lab

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