[gmx-users] solvation_box

shahid nayeem msnayeem at gmail.com
Thu Jan 27 08:00:27 CET 2011

Hi Mark
I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I
solvated this box with genbox using -maxsol 500 and spc216.gro. On
visualization, at this stage itself uniform solvation did not occur and I
got water in one region and chaps molecule spread throughout box but not
inside water. I should have visualized it earlier before going for
minimization. Please help me.
shahid Nayeem

On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> On 01/27/11, *shahid nayeem * <msnayeem at gmail.com> wrote:
> 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.
> 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.
> Mark
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