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

[wezhao at ucalgary.ca]

Hi XAvier,

Thanks for your help! I will try it now.
Have a great day!
Wei

>
> 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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