Re: Sudden expansion of box when continuing NPT simulation

From: Peter Freddolino (
Date: Tue Jan 29 2008 - 12:24:46 CST

Hi Jawahar,
could you please send your config files for the first and second runs? I
have not seen similar behavior before...

Jawahar Neelankatan wrote:
> 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.
> Jawahar
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