Hmm.. Martini proteins should run fine with ~30fs timesteps. Could you check the bonded parameters for the bond listed, and take this to the Martini forum (cgmartini.nl)? @Mark: The Martini forcefield was validated with timesteps between 10 and 40 fs; although some of the parametrised molecules (such as DNA) only work with the smaller timesteps.
Peter On Thu, Apr 14, 2016 at 3:47 PM, James Starlight <jmsstarli...@gmail.com> wrote: > actually I have the same system with the same mdp options simulated in > parallel where I dont have such warnings. so I dont know the sourse > of that error in the latter case > > the only different between two was t_coupling used in equilibration (0.5 > vs 1.0) > > 2016-04-14 15:34 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>: > > Hi, > > > > That depends. Why do you think the increase in integration step is a > valid > > model physics? > > > > Mark > > > > On Thu, Apr 14, 2016 at 3:25 PM James Starlight <jmsstarli...@gmail.com> > > wrote: > > > >> another problem when I try to increase slightly integration step from > >> 0.01 to 0.02 I obtain > >> > >> WARNING 1 [file system.top, line 44]: > >> The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an > >> estimated oscillational period of 9.7e-02 ps, which is less than 5 > times > >> the time step of 2.0e-02 ps. > >> Maybe you forgot to change the constraints mdp option. > >> > >> that is waht related to constraints in my mdp > >> constraints = none > >> constraint_algorithm = Lincs > >> unconstrained_start = no > >> lincs_order = 2 > >> lincs_warnangle = 30 > >> > >> Can I ignore this warning? > >> > >> J. > >> > >> 2016-04-14 10:05 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>: > >> > passing -rdd with a larger value forces mdrun to make larger domain > >> cells, > >> > basically reducing the number of ranks you can use and hampering > >> > parallelization. I don't think it affects the physics. > >> > Reducing the CPU count does the same thing. > >> > > >> > Peter > >> > > >> > On Thu, Apr 14, 2016 at 9:57 AM, James Starlight < > jmsstarli...@gmail.com > >> > > >> > wrote: > >> > > >> >> an question: might the bigger -rdd like 1.8 or 2.0 produce ssmth bad > >> >> in simulation? generally I found that with rdd 1.8 the siduation is > >> >> better, also I reduced number of CPU for that job from 256 to 128 and > >> >> it works OK by now! > >> >> > >> >> Gleb > >> >> > >> >> 2016-04-14 9:40 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>: > >> >> > Hi James, > >> >> > > >> >> > 1) use a newer version of Gromacs > >> >> > 2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn > >> are so > >> >> > long and flexible they occasionally confuse gromacs' domain > >> >> decomposition. > >> >> > > >> >> > Peter > >> >> > > >> >> > On Thu, Apr 14, 2016 at 8:49 AM, James Starlight < > >> jmsstarli...@gmail.com > >> >> > > >> >> > wrote: > >> >> > > >> >> >> Dear Gromacs Users! > >> >> >> > >> >> >> I faced with the problems while simulating of big MARTINI system > of > >> >> >> membrane protein complex within big membrane consisted totally of > 55k > >> >> >> martini CG atoms. > >> >> >> > >> >> >> On the early stage of the NPT equilibration I have a error > >> >> >> > >> >> >> Program g_mdrun_openmpi, VERSION 4.5.7 > >> >> >> Source code file: > >> >> >> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line: > 173 > >> >> >> > >> >> >> Software inconsistency error: > >> >> >> Some interactions seem to be assigned multiple times > >> >> >> For more information and tips for troubleshooting, please check > the > >> >> GROMACS > >> >> >> website at http://www.gromacs.org/Documentation/Errors > >> >> >> ------------------------------------------------------- > >> >> >> > >> >> >> > >> >> >> does the problem is related to paralelization or smth wrong with > >> >> >> setup? Amazing that on the same system without Elnedyn applied I > have > >> >> >> no such promlems at ell. > >> >> >> > >> >> >> Thanks so much for help! > >> >> >> > >> >> >> J. > >> >> >> -- > >> >> >> 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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