Dear All, I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in simple spc water in a dodecahedron box. I could easily walk through till the NVT equilibration step after which every thing seems so right(after 50000 steps with time step of 2fs using V-rescale thermostat the system equilibrates to T=300K). But the NPT equilibration ( for 50000 steps with time step of 2fs using Parrinello-rahman barostat) is crashing( after 10000 steps) with too many LINCS warnings. Looking at the log file I understand there are very high fluctuations in the temperatures after a few steps from the start of the simulation. What can be the possible reason for this kind of a behavior and what can be done to fix it?
-- KRISHNA KISHORE@IIT-MADRAS
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