Hi Afsane,
This might be an issue with the pressure coupling, depending on the compressibility you give for your system and the algorithm that you use for pressure coupling you might see quite large fluctuations in pressure. One idea might be to use temperature coupling to quickly dissipate large energies due to large fluctuations in box size. If you're not already using it you could try a robust temperature coupling with v-rescale with tau-t = 0.1, which is usually recommendable. Using some steps to carefully anneal your system might help as well. To carefully heat your system from 0 to 300K in the first 100ps of the simulation you might use "annealing = single annealing-npoints = 2 annealing-time = 0 100 annealing-temp = 0 300".
Then pressure-pre-equlibrating your system with the Berendsen barostat might be helpful, just don't use it for your production run.
Best, Christian On 2020-04-25 19:16, Afsane Farhadi wrote:
Hi gromacs users I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas is ok (potential energy is about -2e+03))but when I want to run a npt run ,the lincs warning are showing( bond rotate more than 30 degree).I repeated energy minimization but it didn't work right Can any body help me please? Sent from Yahoo Mail on Android
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