[gmx-users] 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
Dallas Warren
dallas.warren at monash.edu
Tue Nov 12 01:11:33 CET 2019
Farideh,
There appears to be a problem with the topology that you are using for the
molecule that explodes.
Look at the pdb files generated at each time the system has exploded. Work
out which group of atoms are moving too far, then look at the topology
around those atoms to identify where the problem is located. Where the
instability has started, there will be something about the topology around
that location which is wrong.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
On Sat, 9 Nov 2019 at 04:17, Farideh Badalkhani Khamseh <
f.badalkhani at modares.ac.ir> wrote:
> Dear GROMACS users.
>
> I am trying to perform MD simulations on a PEGylated dendrimer. At first,
> I performed energy minimization with
>
> emtol = 1000 kJ/mol/nm.
>
> I did not gent any error in EM, NVT (1 ns), and NPT (1 ns) equilibrations.
> But the simulation crashed relatively early (within 1 ns). Therefore, I
> performed successive Steep and CG minimizations until the system was
> minimized at emtol = 80 kJ/mol/nm. Again, I did not get any error during
> NVT and NPT equilibrations. This time production MD crashed after 10 ns and
> I got the following error:
>
> DD step 5489999 load imb.: force 0.2%
> Step Time
> 5490000 10980.00000
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih. LJ-14
> 2.27616e+03 7.97871e+03 6.08238e+03 3.55375e+01 2.21395e+03
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 3.79715e+04 3.35801e+05 -1.16286e+04 -2.68521e+06 8.57466e+03
> Potential Kinetic En. Total Energy Conserved En. Temperature
> -2.29590e+06 4.43034e+05 -1.85287e+06 -1.63147e+06 3.10476e+02
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -1.10990e+02 9.76046e+01 3.84574e-06
>
> Constraint error in algorithm Lincs at step 5491696
> Wrote pdb files with previous and current coordinates
> Constraint error in algorithm Lincs at step 5491698
> Wrote pdb files with previous and current coordinates
> Constraint error in algorithm Lincs at step 5491700
> Wrote pdb files with previous and current coordinates
> Constraint error in algorithm Lincs at step 5491701
> Wrote pdb files with previous and current coordinates
> Constraint error in algorithm Lincs at step 5491702
> Wrote pdb files with previous and current coordinates
> Constraint error in algorithm Lincs at step 5491703
> Wrote pdb files with previous and current coordinates
> Constraint error in algorithm Lincs at step 5491704
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program: gmx mdrun, version 2019.3
> Source file: src/gromacs/ewald/pme-redistribute.cpp (line 282)
> MPI rank: 0 (out of 2)
>
> Fatal error:
> 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off
> out
> of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> The md.mdp file is as follows:
>
> title = G3ACE-16PEG MD
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 50000000 ; 2 * 50000000 = 100 ns
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 5000 ; save coordinates every 10 ps
> nstvout = 5000 ; save velocities every 10 ps
> nstfout = 5000 ; nstvout, and nstfout
> nstenergy = 5000 ; save energies every 10.0 ps
> nstlog = 5000 ; update log file every 10.0 ps
> nstxout-compressed = 5000 ; save compressed coordinates every
> 10.0 ps
> compressed-x-grps = System ; save the whole system
> ; Bond parameters
> continuation = yes ; Restarting after NPT
> constraint_algorithm = lincs ; holonomic constraints
> constraints = h-bonds ; bonds involving H are constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme = Verlet ; Buffered neighbor searching
> ns_type = grid ; search neighboring grid cells
> nstlist = 10 ; 20 fs, largely irrelevant with
> Verlet scheme
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in
> nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (in
> nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen
> thermostat
> tc-grps = Dendrimer Water_and_ions ; two coupling
> groups - more accurate
> tau_t = 0.1 0.1 ; time constant, in
> ps
> ref_t = 310 310 ; reference
> temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in
> NPT
> pcoupltype = isotropic ; uniform scaling of box
> vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in
> bar
> compressibility = 4.5e-5 ; isothermal
> compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
>
> ----------------------------------------------------------------------------------------------------------------------
>
>
> Any help will be greatly appreciated.
>
>
> Kind regards,
>
> Farideh Khamseh
>
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