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How sure are you your coordinates are sane? If gromacs runs (i.e. grompp doesn't throw errors/warnings), and you still get infinite energies and LINCS warnings I guess you have clashes. |
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Hi @pckroon @Boupalik |
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It's been forever since I've had to run a simulation, but the fact that it doesn't work after you start from an equilibrated atomistic structure has me a bit concerned. Maybe @csbrasnett has any insights here? |
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If you're able to energy minimise the system but not start dynamics, it could be worth doing timestep incremental equilibrations, doing a series of eg. 0.002, 0.005, 0.01 ps timesteps starting from each previous step (remember continuation = no and gen_vel = -1 in your mdps after the first run!). Otherwise, it might be worth checking your elastic network by varying the force constant or cutoff, or using a different -eunit when martinizing them. btw, with the new version of cgmartini.nl we have a new martini discussion forum which might be another useful place to discuss such challenges with martini simulations |
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I'll follow those advices. |
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What is the best way to martinize very big structures with more atoms than 99999. I've been trying to do this by splitting my pdb file into various chains and martinizing and combining them, only to face linc errors and infinite energy. What ways do you guys use to martinize very big structures and face no errors in the gromacs simulation?
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