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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