[gmx-users] Simulation Crash...Reg

Kishore kris.vempali at gmail.com
Sun Apr 3 08:41:32 CEST 2011

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?

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