[gmx-users] Importance of -rcon and -dd options when using mdrun with mpi.

[Mark Abraham]

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

> 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.
>
> *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.
>
> *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?
>
> Values which I have tried are relevant or very bad?**
>
> 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://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120314/64be9330/attachment.html>