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

[PAVAN PAYGHAN]

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.





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/20120314/2101a762/attachment.html>