[gmx-users] nstlist and performances

[Mark Abraham]

On Tue, Nov 19, 2013 at 6:12 AM, rajat desikan <rajatdesikan at gmail.com>wrote:

> 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...
>

Bear in mind that their conclusions are based on unbuffered neighbour lists
(which are obviously a problem when using charge groups), and GROMACS
4.0.5, which was almost three years old at the time they submitted... There
are reasons why the 4.6 Verlet scheme does not use charge groups and
defaults with a buffer. ;-)

Mark


> 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
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