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.abra...@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.fku...@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 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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