I'm having trouble with a system that runs in NVT but doesn't run in NPT ensemble. I have tried few atoms (100,000 aprox) and I have no problem. But when my system gets bigger (400,000) I have LINCS error, so I first tried making the box a lot bigger and putting a radius of 0.9 nm when I solvated the system but the output still had the number of molecules according to the size of the box, which I didn't want. So I tried another software for making my initial configurations, now I had a box (220 Angstroms side) with aprox 400,000. I tried to run it in NPT ensemble so that it acquired the right density through time, but I still had LINCS. So I changed for NVT ensemble to equilibrate it and it ran for a few (2) nanoseconds, but when I change to NPT I still have LINCS and doesn't run!

I was thinking about changing the pressure to 1000 and then little by little getting to 1 so that my system gets the right density. But I haven't been able to run in NPT ensemble.

Any ideas?