[gmx-users] Simulation crashed

Sheikh Imamul Hossain imamul_math at yahoo.com
Tue May 1 05:48:29 CEST 2018

Hi All,
I am doing CG simulation on lipid monolayer with gold nanoparticles (AuNP). I have done the simulation with single 3nm AuNP and two lipid monolayers apart by 6nm water slab. The NP was placed 6nm above from the upper monolayer. This system is also fine with 3NPs. I have an another system with same number of lipids (1023 in each monolayer) but this time the water thickness was 16nm and the number of NPs were 36 in each side(36 for upper layer and 36 for lower layer). The distance between two NPs was 0.5nm and the box dimension was 25x25x60mn. During equilibration at 0mN/m surface tension with low time step 10fs and tau_p=12 the simulation crashed though position restraints was applied to AuNP. The system also got crashed without NPs. I don’t understand whether the problem is for high water thickness or number of NPs. I have also tried with 4NPs (10nm apart from each other) and the this time the monolayer collapsed. All the system were minimized before equilibration.
Thanks in advance.

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