[gmx-users] Protein simulation, improve GPU/CPU ratio

[Justin Lemkul]

On 11/3/16 1:48 PM, Matilde Viegas wrote:
> Dear all,
>
> I have a few questions regarding a simulation system containing a protein
> in a box of water, with ions. Just like the lysozyme tutorial:
>
> my system is a 5000 residue enzyme (75600 atoms), in a triclinic TIP3P
> water box of a total 1567103 atoms (around 500000 water molecules). My
> input is:
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1000.0        ; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization) steps to
> perform
> define = -DFLEXIBLE
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist             = 40            ; Frequency to update the neighbor list
> and long range forces
> cutoff-scheme   = Verlet
> ns_type             = grid              ; Method to determine neighbor list
> (simple, grid)
> coulombtype         = Reaction-Field    ; Treatment of long range
> electrostatic interactions
> rcoulomb            = 1.0               ; Short-range electrostatic cut-off
> rvdw                = 1.0               ; Short-range Van der Waals cut-off
> pbc                     = xyz           ; Periodic Boundary Conditions
> (yes/no)
>
> Unfortunately, my GPU/CPU ratio is 16= Force evaluation time GPU/CPU:
> 345.675 ms/20.818 ms = 16.605
>
> Any ideia on how I can improve the ratio?
>

Energy minimization is a poor way to evaluate performance of your hardware.  Do 
a real MD run and inspect the .log file.  The end has a detailed performance 
breakdown of exactly how mdrun spent all its time.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================