normal Fatal error when running DOPC membrane

  • Marks
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8 years 3 months ago #5450 by Marks
I have performed a simulation of a nanoparticle interacting with the DOPC membrane based on MARTINI CG model, also I used PME method for the electrostatic interactions and the job was done on a 16-core node. The time step is 20 fs. The lipid bilayer consists of 1000 lipid and 43000 water. However, the simulation crashed after about 500 ns.
The error message is given by:
DD step 26629999 vol min/aver 0.814 load imb.: force 0.6%

Step Time Lambda
26630000 532600.00000 0.00000

Energies (kJ/mol)
Bond Angle G96Angle LJ (SR) Coulomb (SR)
1.93538e+04 5.55346e+02 8.59136e+03 -1.34473e+06 -8.77691e+02
Coul. recip. Potential Kinetic En. Total Energy Temperature
-3.97243e+03 -1.32108e+06 2.11894e+05 -1.10918e+06 3.09115e+02
Pressure (bar)
-1.08685e+01

Not all bonded interactions have been properly assigned to the domain decomposition cells

A list of missing interactions:
G96Angle of 19936 missing 1

A list of missing interactions:
G96Angle of 8000 missing 1

Molecule type 'DOPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms 2 3 5 global 4725 4726 4728
Program mdrun, VERSION 4.5.4
Source code file: domdec_top.c, line: 356

Fatal error:
1 of the 32321 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors

"Three Little Fonzies" (Pulp Fiction)
I have performed the simulation many times, and such error is appeared in each simulation. i hope that you can give me some advise, and I will appreciate significantly for your kindness.

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8 years 3 months ago #5452 by helgi
Replied by helgi on topic Fatal error when running DOPC membrane
Hello, hello,

This is more likely a GROMOS issue then a Martini issues – GROMOS is super fast but, especially when you are pushing it with respect to time step etc. spurious instabilities can occur. For this I would suggest restring on the previous state file and I would also suggest adding –rdd 1.4 (or even 1.6) limiting the minimum size of the domains.

Cheers,
- Helgi

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