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

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 11:32:51 CET 2012

On 11/1/12 5:06 PM, Steven Neumann wrote:
> On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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
> Thanks for your reply. I am trying to get parametrs for coarse grained
> model so I want to repeat this procedure until covergence. Do you
> think NVT could be used for this purpose?

I don't have nearly enough information to make any comment about that, sorry.



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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