[gmx-users] Re: Importance of -rcon and -dd options
PAVAN PAYGHAN
pavanapex at gmail.com
Thu Mar 15 18:01:38 CET 2012
>
>
>> > > 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
>> > >
>> > >
>> >
>>
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