[gmx-users] md.log interpretation
Nizar Masbukhin
nizar.fkub08 at gmail.com
Thu Nov 6 12:46:29 CET 2014
I have tried running simulation with zero cutoff and zero nstlist and
simple ns. That was very very slow, however.
anyway thanks for the reply.
On Nov 5, 2014 9:38 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> Hi,
>
> I am not familiar with the implementation details, but I would assume there
> is a dependency on rcoulomb of the cost of the Born force chain rule. You
> can check this by trying different values. It might be faster to use
> infinite cutoffs (see manual) so that the algorithm does not need to
> search.
>
> Mark
>
> On Tue, Nov 4, 2014 at 1:34 AM, Nizar Masbukhin <nizar.fkub08 at gmail.com>
> wrote:
>
> > Dear gromacs users,
> > I've just finished my NVT equilibration in implicit solvent. From
> md.log, i
> > see that most of time were used to calculate Forces (of Born force chain
> > rule). Could someone explain to me why calculating it takes so long?
> >
> > mdp setting:
> >
> > integrator=md
> > dt=0.004
> > nstep=2500000
> > bd-frict=50
> > rlist=5
> > rvdw=5
> > rcoulomb=5
> > nstlist=40
> > implicit-solvent=GBSA
> > gb-alogarithm=still
> > nstgbradii=40
> > gbradii=5
> > gb-epsilon-solvent=80
> > gb-salt-conc=0.2
> > sa-algorithm=ace-approximation
> > sa-surface-tension=2.05
> > constraints=all-bonds
> > constraints-algorithm=LINCS
> > lincs-order=12
> >
> >
> > md.log
> >
> > M E G A - F L O P S A C C O U N T I N G
> >
> > NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels
> > RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table
> > W3=SPC/TIP3p W4=TIP4p (single or pairs)
> > V&F=Potential and force V=Potential only F=Force only
> >
> > Computing: M-Number M-Flops %
> Flops
> >
> >
> -----------------------------------------------------------------------------
> > NB VdW [V&F] 32677.013279 32677.013
> 0.0
> > NB VdW [F] 1740991.575264 1740991.575
> 0.3
> > NB VdW & Elec. [V&F] 1192677.312698 1192677.313
> 0.2
> > NB VdW & Elec. [F] 106409048.599622 106409048.600
> 17.9
> > 1,4 nonbonded interactions 20035.628466 1803206.562
> 0.3
> > Born radii (Still) 1999216.232742 93963162.939
> 15.8
> > Born force chain rule 25548182.811729 *383222742.176*
> > 64.4
> > NS-Pairs 64906.572700 1363038.027
> 0.2
> > CG-CoM 205.506576 616.520
> 0.0
> > Propers 15168.313980 3473543.901
> 0.6
> > Impropers 637.980588 132699.962
> 0.0
> > Pos. Restr. 3830.053530 191502.676
> 0.0
> > Virial 82.695471 1488.518
> 0.0
> > Stop-CM 82.214752 822.148
> 0.0
> > Calc-Ekin 822.011152 22194.301
> 0.0
> > Lincs 4696.969329 281818.160
> 0.0
> > Lincs-Mat 229529.791548 918119.166
> 0.2
> > Constraint-V 9393.938658 75151.509
> 0.0
> > Constraint-Vir 46.973979 1127.375
> 0.0
> > Virtual Site 3 615.868824 22787.146
> 0.0
> > Virtual Site 3fd 791.205144 75164.489
> 0.0
> > Virtual Site 3fad 168.761208 29701.973
> 0.0
> > Virtual Site 3out 1893.632256 164746.006
> 0.0
> > Virtual Site 4fdn 576.418152 146410.211
> 0.0
> > (null) 476.315439 0.000
> 0.0
> >
> >
> -----------------------------------------------------------------------------
> > Total 595265438.267
> 100.0
> >
> >
> -----------------------------------------------------------------------------
> >
> >
> > R E A L C Y C L E A N D T I M E A C C O U N T I N G
> >
> > On 1 MPI rank
> >
> > Computing: Num Num Call Wall time Giga-Cycles
> > Ranks Threads Count (s) total sum %
> >
> >
> -----------------------------------------------------------------------------
> > Vsite constr. 1 1 1085001 96.421 385.432
> 0.2
> > Neighbor search 1 1 27126 915.964 3661.462
> 2.1
> > Force 1 1 1085001 *39317.742* 157168.118
> > 91.3
> > Vsite spread 1 1 1095852 142.563 569.880
> 0.3
> > Write traj. 1 1 11030 425.764 1701.942
> 1.0
> > Update 1 1 1085001 96.742 386.714
> 0.2
> > Constraints 1 1 1085001 1311.720 5243.449
> 3.0
> > Rest 766.404 3063.612
> 1.8
> >
> >
> -----------------------------------------------------------------------------
> > Total 43073.320 172180.608
> 100.0
> >
> >
> -----------------------------------------------------------------------------
> >
> > Core t (s) Wall t (s) (%)
> > Time: 41985.828 43073.320 97.5
> > 11h57:53
> > (ns/day) (hour/ns)
> > Performance: 8.706 2.757
> > Finished mdrun on rank 0 Tue Nov 4 03:27:26 2014
> >
> >
> > I know, for someone this question is less important, but for me
> performance
> > is important.
> >
> > --
> > Thanks
> > My Best Regards, Nizar
> > Medical Faculty of Brawijaya University
> > --
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