[gmx-users] solvation_box

Mark Abraham mark.abraham at anu.edu.au
Thu Jan 27 07:06:12 CET 2011

On 01/27/11, shahid nayeem  <msnayeem at gmail.com> wrote:
> Dear AllI am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do.


You haven't told us how you've solvated the system (e.g. with genbox), that it looked OK when you visualized it between each step, and that you're sure your observations cannot be rationalized as a periodicity artefact.

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