[gmx-users] solvation_box_preparation

shahid nayeem msnayeem at gmail.com
Thu Jan 27 14:33:53 CET 2011

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
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

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