On 12/21/12 2:57 PM, emmanuelle wrote:
Thanks for your reply.
1.My cutoffs are OK. Indeed, changing them leads to the same problem.
This outcome points to a topology or configuration issue.
2.My original box is 20nm in length. I generate it using genconf to avoid
any lack of memory that genbox could provide for a system of such a size.
Then I use editconf to reach the required density of 1000g/l.
Scaling with editconf can shorten or elongate bonds and has never been a very
robust approach in my hands. It is better to generate a box that has a
reasonable density and use sufficient equilibration to achieve the target value
(within the accuracy of the force field being used).
2b.Atom 13090 is a H atom of an MEA molecule (HO-CH2-CH2-NH2). More
specifically, it is the hydrogen directly bonded to the oxygen.
Surprisingly, when I simulate a similar system for which I only substitute
the monoethanolamine molecules by ethanolamine molecules, everything works
perfectly fine.
Could you help me on this?
Probably the editconf scaling adjusted the coordinates in a bad way.
-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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