[gmx-users] genbox problem with micelle

[Alif M Latif]

Dear GROMACS users and developers..

I'm trying to run MD simulation on a micelle structure, which i've built using Packmol. The problem is when i use genbox to solvate the system using SPC water, the water came inside the micelle, and my simulation didn't produce any significant changes to the structure (the behavior of lipids which are lipophilic should squeezed the water molecules outside the micelle structure). I'm wondering if i can tell genbox not to put water molecule inside the micelle...can i?.. :-p

Thanks 4 reading...any comments and suggestion will be greatly appreciated..

Alif


       
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