[gmx-users] Biphasic Systems

[Justin Lemkul]

On 10/30/12 5:21 AM, Davoud Zare wrote:
> Dear Gmx Users,
> I made a biphasic system with water and hexane following Justin tutorial  (800 hexane molecules) ,after adding the peptides in water phase, the number of the hexane molecules were reduced and some of them were shifted to the other side of water molecules (not at the interface of oil-water).
> any comments on this?

What commands did you use to produce the system?  If done properly, this should 
not have happened.  Hexane molecules traversing the box is likely just a PBC 
effect, but that would only occur over the course of a simulation (not simple 
system construction) and should be transient.

-Justin

-- 
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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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