[gmx-users] solvation_box

shahid nayeem msnayeem at gmail.com
Thu Jan 27 05:31:30 CET 2011

Dear All
I 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.
Shahid nayeem
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