[gmx-users] solvation_box

shahid nayeem msnayeem at gmail.com
Thu Jan 27 08:17:02 CET 2011

I forgot to mention that when I prepared urea_water box then also I got
similar box of water in one region and urea in other region separated from
it. But on minimization and following simulated annealing
and equilibration I got a uniformly mixed urea water box.
Shahid Nayeem

On Thu, Jan 27, 2011 at 12:30 PM, shahid nayeem <msnayeem at gmail.com> wrote:

> Hi Mark
> Thanks.
> 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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