On 4/19/13 2:57 PM, Shima Arasteh wrote:
Thanks so much for your replies. I appreciate you.
Do you think that more NPT equilibration might solve the problem? or wont work?
I have no idea at what point you are in your procedure that is crashing. I'm
not going to make some blind assessment of "do more NPT" or some random thing.
If you just completed the EM as you posted, proceed with whatever equilibration
protocol you believe to be sufficient. There is no one single answer here. If
you're jumping straight into MD after the EM you showed, you need to start your
equilibration over again completely.
-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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