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