[gmx-users] nstlist and performances
rajat desikan
rajatdesikan at gmail.com
Tue Nov 19 14:50:29 CET 2013
Hi Mark,
That is a valuable suggestion indeed. By default, most users (I assume; I
could be wrong) use the original forcefield recommendations. What is your
opinion of using buffered Verlet lists (adding cutoff-scheme = Verlet to
the .mdp) along with the original FF recommendations (say Amber FF)?
Thanks,
On Tue, Nov 19, 2013 at 4:52 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> 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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--
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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