[gmx-users] nstlist and performances

[rajat desikan]

Hi,
I would be very careful about increasing nstlist for big systems. This can
lead to nonphysical phenomena, especially for highly anisotropic systems.
Check out http://pubs.acs.org/doi/abs/10.1021/ct3001359  There are other
papers too...


On Mon, Nov 18, 2013 at 9:50 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Mon, Nov 18, 2013 at 3:58 PM, Riccardo Concu <ric.concu at gmail.com>
> wrote:
>
> > Dear all,
> > I'm running a simulation of a quite big system and is running very low
> > 2ns/day. I need to boost-up the simulation speed but i don't know how. I
> > tried to use nstlist=10 but the system crash due to too many lincs
> > warning. Previously I minimized the system, then annealed and now i need
> > to run the production. All the statistics of the minimization step and
> > the anneling step seems good. Below I have attached the .mdp file.
> > Thank you,
> > Riccardo
> >
> > integrator               = md
> > tinit                    = 0
> > dt                       = 0.002
> > nsteps                   = 2000000;4ns
> > comm-mode                = Linear
> > nstcomm                  = 10
> > comm-grps                = System
> > nstxout                  = 25000
> > nstvout                  = 25000
> > nstfout                  = 25000
> > nstlog                   = 25000
> > nstenergy                = 25000
> > nstxtcout                = 25000
> > xtc-precision            = 25000
> > xtc-grps                 = System
> >
>
> Writing output is not free - choose to write the kinds of data you actually
> want.
>
>
> > energygrps               = NAP NA WAT MET SI3 I LI+
> >
>
> This can be costly - do this in an mdrun -rerun, on only the frames you
> want, if you actually need it.
>
>
> > nstlist                  = 5
> > ns_type                  = grid
> > pbc                      = xyz
> > periodic_molecules       = no
> > rlist                    = 0.9
> > coulombtype              = PME
> > rcoulomb                 = 0.9
> > vdw-type                 = Cut-off
> > rvdw                     = 0.9
> > fourierspacing           = 0.12
> > fourier_nx               = 0
> > fourier_ny               = 0
> > fourier_nz               = 0
> > pme_order                = 6
> >
>
> Why? Nobody does this AFAIK
>
>
> > ewald_rtol               = 1e-5
> > optimize_fft             = yes
> > Tcoupl                   = v-rescale
> > tc-grps                  = System
> > tau_t                    =  0.1
> > ref_t                    = 298
> > Pcoupl                   = Parrinello-Rahman
> > Pcoupltype               = Isotropic
> > tau_p                    = 1
> > compressibility          = 4.5e-5
> > ref_p                    = 1.01325
> > gen_vel                  = yes
> >
>
> I'd follow the advice here
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
> about
> equilibrating, which should relax the effective nstlist constraint, because
> you're not doing big volume changes with a marginally stable barostat.
>
> Then I'd do my measuring of performance over a production run, and look at
> the reports at the end of the .log file to see what's taking time that
> might be inappropriate.
>
> Mark
>
>
> > gen_temp                 = 298
> > gen_seed                 = 173529
> > constraints              = all-bonds
> > constraint-algorithm     = Lincs
> > lincs-order              = 4
> > lincs-iter               = 1
> >
> >
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore