[gmx-users] Re.Importance of -rcon and -dd options when
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Mar 15 08:04:09 CET 2012
On 15/03/2012 5:36 PM, PAVAN PAYGHAN wrote:
>
>
> On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote:
> >
> > 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.
>
> 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
> >
> >
>
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