Re: expansion of solvation box at high temperature

From: Nicholas Musolino (
Date: Sun Oct 17 2010 - 08:29:06 CDT

Dear mjyang:

On Oct 17, 2010, at 3:03 AM, mjyang wrote:
> I performed a simulation of a protein + TIP3 water system at 600K. But after 2 ns production run under NPT ensemble, the volume of solvation box expanded by more than 1000 times and the mass density reduced from 1.05909 g/cm^3 to 0.000607189 g/cm^3. I am not sure whether this phenomenan is caused by NPT ensemble at hight temperature or any other factors

Your system vaporized. Boiled! So you're right about the cause being high temperature.

To provide helpful advice, we will need to see you pressure control parameters, and your temperature control parameters, from your NAMD input file.

Did you gradually heat up to 600 K from a low temperature? Or just set the thermostat there, and run? The first option will usually be more stable, in practical terms.

Also, can you share why you're trying to simulate at 600 K? Is this for some kind of simulated annealing procedure?

Thanks and good luck,
Nicholas Musolino

Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT | 617-253-6675 | Room E19-528

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