[gmx-users] solvation_box_preparation

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 27 14:36:38 CET 2011

shahid nayeem wrote:
> Dear All
> I am sending this mail again on user list because my reply to Mark’s
> query was not uploaded on the list.
> Original messge:
> 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.
> Reply to query.
> I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox
> –ci 7 chaps.gro).Then I solvated the output box  with genbox using
> -maxsol 500 and spc216.gro. On visualization, at this stage itself
> uniform solvation did not occur (I got water in one region and chaps
> molecule in other region) but I observed a similar situation while

If your box was not completely solvated, then don't use -maxsol.  A box of 6x6x6 
nm should require more than 500 molecules of water to fill.  If you're trying to 
achieve some specific mole fraction or concentration, then re-figure your box size.


> preparing 10M urea salvation box. This was followed by 1ns simulated
> annealing from temp 300K to 0K and pressure 100 bar, then 1ns
> simulated annealing from temp. 0k to 300k and then ins equilibriation
> at this temperature. In case of urea finally I got uniformly solvated
> urea_water_box but in chaps I couldn’t get it.
> Shahid Nayeem


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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