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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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