[gmx-users] solvation_box_preparation

shahid nayeem msnayeem at gmail.com
Fri Jan 28 05:51:20 CET 2011

Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.
Please help.
shahid Nayeem

On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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.
> -Justin
>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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