[gmx-users] minimization problem

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 8 15:35:54 CET 2009

Hongyan Xiao wrote:
> Hi,
> I has used the periodic boundary conditions and correct em.mdp 
> file. However, the minimized result is water/decane/water, while I set 
> decane/water/decane as the initial system . I cannot understand the 
> reason. Please give me some constructive suggestion! Thanks!

Your system is probably not centered in the box, and thus PBC is reconstructing 
it.  Use ngmx to see how Gromacs is viewing your system.


> H. Y. Xiao
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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