> > >> > > Dear Gromacs Users, >> > > >> > > I am running mdrun on single node with 8 CPU and getting >> > following error >> > > >> > > Fatal error:- >> > > >> > > D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are >> > > connected via constraints from the neighbouring cells. >> > > >> > > This probably means your constraint length are too long compared >> to >> > > the domain decomposition cell size. >> > > >> > > Decrease the number of domain decomposition grid cells or lincs >> > order. >> > > >> > >> > The .log file has a detailed analysis of how DD is setting things >> up. >> > You need to make sure that this output is sensible for your system. >> > >> > You should also desist from using P-R pressure coupling during >> > equilibration (i.e. with velocity generation), as warned in the >> manual >> > section on pressure coupling. Perhaps your system is blowing up. >> > >> > Mark >> > >> > Dear Mark, >> > >> > Thanks for the reply. >> > I have successfully done the equilibration run ,while doing >> > production run I am gettiing above error (almost after 10 ns run). >> > Also It would be worth working if you explain the importance -rcon >> > value and other things that I have asked . >> >> A description of your system, GROMACS version and objective are >> important to solving the problem. I don't think we've seen those. Nobody >> wants to spend time talking about DD options if you are trying to run a >> system with 1000 atoms on 8 processors. By not describing fully, you >> make it easy for people to not be bothered. >> >> > Dear Mark, > > Thanks for the reply, at the same time I am sorry for providing the > incomplete information > (Next time onward I will make it a habit to describe the problem > properly as you said). > As you asked my system contains about 425000 atoms ( protein + Lipid > +SOL). The gromacs version is 4.5.3 . > In Objectives, I have successfully reached up to NPT equilibration run > step, now I want to continue the same for production run. > If this information is sufficient enough please reply. > > > > >> > Regards, >> > >> > Pavan >> > >> > > For solving this problem following are the attempts by me. >> > > >> > > *1] Decreasing grid cell size:-* >> > > >> > > As per the suggestion in error, I tried to decrease the grid >> > cells by >> > > option -dd from 8 1 1 to 6 1 1 , it has thrown following error.. >> > > >> > > Fatal error:-The size of the DD grid (6) does not match the >> > number of >> > > nodes(8). >> > > >> > > Can you please suggest any better way to overcome this for >> > decreasing >> > > grid cell size. >> > >> >> You can't decrease the number of DD cells since you need one per >> processor. Maybe you are trying to parallelize a system that is too >> small for this number of processors, which brings us back to needing a >> description of your system. >> >> > > >> > > *2] -rcon option:* >> > > >> > > What is the correlation between the -rcon value with DD cell >> > > size(Directly or inversely proportional ) , for the problem >> entitled >> > > above what should be the strategy (to decrease or to increase >> > rcon value). >> > > >> > > If one changes the -rcon value will it affect the lincs accuracy, >> or >> > > in other words the run will hold the same continuation or any >> change >> > > in it. >> > > >> > > For changing the -rcon value the reference of previous log file >> i.e. >> > > Estimated maximum distance required for p-lincs say 0.877, so >> > one can >> > > increase than what has been estimated. >> > >> >> You need to read mdrun -h about -rcon. You need to be trying to increase >> the ratio of cell size to constraint length, per the error message. >> >> > > >> > > *3] lincs_order and lincs_iter :* >> > > >> > > ** >> > > >> > > If we don't want to deteriorate the lincs accuracy (1+ >> > > lincs_iter)*lincs_order has to remain constant , In my case >> > > >> > > With lincs_order = 4 and lincs_iter =1 I got above error. So I >> > > decreased lincs _order (2) and increased lincs_iter(3) >> > proportionally. >> > > What I am following is right or I have misunderstood it. If so >> > please >> > > correct it. Can this value be fraction? >> > >> >> The values must be integers. >> >> > > Values which I have tried are relevant or very bad?** >> > >> >> That is a correct approach for maintaining LINCS accuracy and trying to >> decrease the required constraint length, however it may not help solve >> the underlying problem. >> >> Mark >> >> > > >> > > Please explain it. >> > > >> > > If the same problem can be solved by any other methodology please >> > > explain it. >> > > >> > > *Please see the mdp file details.* >> > > >> > > >> > > integrator = md >> > > >> > > nsteps = 10000000 >> > > >> > > dt = 0.002 ; 2 fs >> > > >> > > ; Output control >> > > >> > > nstxout = 1000 ; >> save >> > > coordinates every 2 ps >> > > >> > > nstvout = 1000 ; >> save >> > > velocities every 2 ps >> > > >> > > nstxtcout = 1000 ; xtc compressed >> > > trajectory output every 2 ps >> > > >> > > nstenergy = 1000 ; save energies >> > every 2 ps >> > > >> > > nstlog = 1000 ; update log >> file >> > > every 2 ps >> > > >> > > ; Bond parameters >> > > >> > > continuation = yes ; Restarting after NPT >> > > >> > > constraint_algorithm = lincs ; holonomic constraints >> > > >> > > constraints = all-bonds ; all bonds (even heavy >> > atom-H >> > > bonds) >> > > >> > > lincs_iter = 1 ; accuracy >> > of LINCS >> > > >> > > lincs_order = 4 >> > > >> > > ; Neighborsearching >> > > >> > > ns_type = grid >> > > >> > > nstlist = 5 >> > > >> > > rlist = 1.2 >> > > >> > > rcoulomb = 1.2 >> > > >> > > rvdw = 1.2 >> > > >> > > ; Electrostatics >> > > >> > > coulombtype = PME >> > > >> > > pme_order = 4 >> > > >> > > fourierspacing = 0.16 >> > > >> > > ; Temperature coupling is on >> > > >> > > tcoupl = Nose-Hoover >> > > >> > > tc-grps = Protein P SOL_NA_CL ; three >> > > coupling groups - more accurate >> > > >> > > tau_t = 0.5 0.5 0.5 >> > > >> > > ref_t = 323 323 323 >> > > >> > > group, in K >> > > >> > > ; Pressure coupling is on >> > > >> > > pcoupl = Parrinello-Rahman ; Pressure coupling >> > on in NPT >> > > >> > > pcoupltype = semiisotropic ; uniform >> > > scaling of x-y box vectors, independent z >> > > >> > > tau_p = 2.0 ; time >> > > constant, in ps >> > > >> > > ref_p = 1.0 1.0 ; >> > reference >> > > pressure, x-y, z (in bar) >> > > >> > > compressibility = 4.5e-5 4.5e-5 ; isothermal >> > compressibility, bar^-1 >> > > >> > > ; Periodic boundary conditions >> > > >> > > pbc = xyz ; 3-D PBC >> > > >> > > ; Dispersion correction >> > > >> > > DispCorr = EnerPres ; account for cut-off vdW scheme >> > > >> > > ; Velocity generation >> > > >> > > gen_vel = yes >> > > >> > > ** >> > > >> > > Pavan >> > > >> > > >> > >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20120315/4f8811bc/attachment.html >> >> ------------------------------ >> >> -- >> gmx-users mailing list >> [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> End of gmx-users Digest, Vol 95, Issue 97 >> ***************************************** >> > >
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