Sudden expansion of box when continuing NPT simulation

From: Jawahar Neelankatan (
Date: Mon Jan 28 2008 - 12:11:52 CST

Hi all,
I am seeing some strange behavior in my NPT simulation that i hope someone who might have experienced this before could perhaps help me with.

My first simulation is a combined simulation in which I do minimization, then heating, then 200ps NVT equilibration and then about 1.5 ns NPT simulation. The simulation ended and I wanted to continue it in the NPT ensemble so I created a new configuration file with the same parameters as before, with NPT pressure controls set to EXACTLY the same values as they were previously. I even used the same seed as in the previous simulation.

But I notice that as soon as the new NPT simulation (continuation of the old one) starts, there is a sudden expansion in the box size and the box size then stays fairly constant at that new value. This is strange because, in the previous simulation, the NPT ensemble had run for 1.5 ns at a lower and fairly constant box size. But as soon as I do the new NPT simulation (continuation of the old one), the box size suddenly becomes larger. This doesn't make sense because the continuation of a simulation is supposed to exactly mimic the behavior of the previous simulation if that simulation was allowed to run longer. A sudden rise in the box size just wouldn't be likely to happen if the previous simulation was allowed to run longer, so it doesn't make sense for it to happen as soon as the simulation is continued with a different configuration file.

Could anyone please tell me if this is normal or, if not, why it is happening ? Thanks all.

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