On Tue, Nov 19, 2013 at 2:50 PM, rajat desikan <rajatdesi...@gmail.com>wrote:
> Hi Mark, > That is a valuable suggestion indeed. By default, most users (I assume; I > could be wrong) use the original forcefield recommendations. Indeed, though establishing whether different programs can and do implement equivalent algorithms is very difficult. > 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)? > It would seem to me to be a no-brainer, but there are lots of details to check. For example, Amber12 offers skinnb, which would seem to play the role of the desired buffer, but mostly the force fields were parameterized with an earlier version (see primary literature for details), and it is that version that is (somewhat) important. However, since most of the force fields were parametrized without PME, or even long-ranged dispersion corrections, the point is fairly moot. There must be many kinds of error compensation in the parameters. Inferring transferability of a force field from its * development implementation (e.g. the simulation code version), * model physics (e.g. long-range treatment), and/or * target simulations (e.g. peptide in water vs aqueous protein folding vs membrane protein) is a very risky business. I applaud the kind of independent testing in the link you suggested - I think there is far too much hope-based MD simulation going on. If there's a simulation package that readily does broken simulations, the community needs to know so the problem can be solved (one way or another). That means people being open and communicating :-) I would argue that GROMACS 4.6+Verlet(+ default buffer) is a better implementation of the desired kind of model physics than any code doing anything unbuffered. Whether the force field can live up to that on a given system is unknown until it is observed. Mark > > Thanks, > > > On Tue, Nov 19, 2013 at 4:52 PM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > On Tue, Nov 19, 2013 at 6:12 AM, rajat desikan <rajatdesi...@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.abra...@gmail.com > > > >wrote: > > > > > > > On Mon, Nov 18, 2013 at 3:58 PM, Riccardo Concu <ric.co...@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 > > > > > > > > > > > > > > > -- > > > > > gromacs.org_gmx-users mailing list > > > > > gromacs.org_gmx-users@maillist.sys.kth.se > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > -- > > > > gromacs.org_gmx-users mailing list > > > > gromacs.org_gmx-users@maillist.sys.kth.se > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > -- > > > Rajat Desikan (Ph.D Scholar) > > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > > Dept. of Chemical Engineering, > > > Indian Institute of Science, Bangalore > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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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