On 11/1/12 5:06 PM, Steven Neumann wrote:
On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul <jalem...@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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