[gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water

wezhao at ucalgary.ca wezhao at ucalgary.ca
Tue Feb 8 20:56:16 CET 2011

Dear All,

I have performed a simulation of POPC with polarisable water model in
presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for the
electrostatic interactions and the job was done on a 8-core node with
domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and
16000 water. However, the simulation crashed after about 100 ns.

The error message is given by:
DD  step 5103999 load imb.: force  5.1%

           Step           Time         Lambda
        5104000   102080.00000        0.00000

   Energies (kJ/mol)
           Bond       G96Angle        LJ (SR)   Coulomb (SR)      Potential
    1.18271e+04    6.29597e+04   -4.34519e+05   -3.22701e+05   -6.82433e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    1.66874e+05   -5.15560e+05    3.10498e+02    1.50257e+01    1.85079e-04

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

A list of missing interactions:
            G96Angle of  19936 missing      1

Molecule type 'POPC'
the first 10 missing interactions, except for exclusions:
            G96Angle atoms    4    5    6      global  3696  3697  3698

Program mdrun_s_mpi, VERSION 4.0.7
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 56736 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance (1
nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs
and tabulated bonds also see option -ddcheck

I turned on PME for testing, but it crashed within 1 ns. Could somebody
give me some suggestion on how to solve this problem?

Wei Zhao

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