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Simulation crashed
- Imamul
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5 years 11 months ago #7634
by Imamul
Simulation crashed was created by Imamul
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.
Imamul
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.
Imamul
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- riccardo
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5 years 11 months ago #7635
by riccardo
Replied by riccardo on topic Simulation crashed
Hi Imamul,
It sounds like they are pretty close. How do you compute this distance? Mind that the diameter of a normal (N) Martini bead is 2**(1/6)*0.47 = 0.53 nm (where 0.47 is the sigma of N-beads), so 0.5 nm means the NPs may be already so close to be repelling each other, i.e., it might be that your system is too packed.The distance between two NPs was 0.5nm
However, I am not sure why your system crashed also without NPs. Which kind of crash do you get? Did you try to visually inspect the system for anomalies?The system also got crashed without NPs.
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- Imamul
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5 years 11 months ago #7636
by Imamul
Replied by Imamul on topic Simulation crashed
Hi Riccardo,
Thanks for your reply. I have resolved the issue of the system without NPs. Again thanks for your valuable advice on NPs.
Regards
Imamul
Thanks for your reply. I have resolved the issue of the system without NPs. Again thanks for your valuable advice on NPs.
Regards
Imamul
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