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
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