[gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water
wezhao at ucalgary.ca
wezhao at ucalgary.ca
Wed Feb 9 17:14:31 CET 2011
Thanks for your help! I will try it now.
Have a great day!
> 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.
> 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
>> 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)
>> 1.18271e+04 6.29597e+04 -4.34519e+05 -3.22701e+05
>> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd
>> 1.66874e+05 -5.15560e+05 3.10498e+02 1.50257e+01
>> 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
>> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for
>> 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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