[gmx-users] T - Annealing at NP - cell expands
s.neumann08 at gmail.com
Thu Nov 1 22:06:27 CET 2012
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.
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?
> 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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