[gmx-users] minimization problem

[Justin A. Lemkul]

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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-- 
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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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