[gmx-users] T - Annealing at NP - cell expands

Justin Lemkul jalemkul at vt.edu
Thu Nov 1 21:45:02 CET 2012

On 11/1/12 4:36 PM, Steven Neumann wrote:
> Dear Gmx Users,
> I have system with protein in water. I equlibrated it in at 300 K and
> 1 bar for 5 ns with position restrained of protein heavy atoms. I run
> script at NP and increasing temperature from 300K to 600 K with
> changing temperature of 1 Kelvin every 1000 steps. Then temperaure is
> set to be 600 K for another 4 ns to cool it down after to 300K within
> 2 ns.
> System fails when the temperature reached 600K - my box is being
> expanded during the temperature increase TWICE! This is why it fails
> and my job terminates.
> Would you suggest something?

A complete .mdp file would be useful here (just in case), although the observed 
behavior doesn't sound too unusual to me.  Under constant pressure, when you 
heat a liquid, what happens?  600K is well above the boiling point of water, so 
it sounds to me like your unit cell is simply responding to what you're doing. 
Perhaps you should be using NVT, but I don't know what your purpose for this 
procedure is.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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