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
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