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

[XAvier Periole]

Hi Wei,

What you need here is to increase the rdd to 1.4/1.5 nm. You can do that using the -rdd option of mdrun. 

Turning pme on would have no effect. 

XAvier. 

On Feb 8, 2011, at 20:56, wezhao at ucalgary.ca wrote:

> 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?
> Thanks!
> 
> Wei Zhao
> 
> 
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