[gmx-users] solvation_box_preparation

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 28 06:29:26 CET 2011

On 28/01/2011 3:51 PM, shahid nayeem wrote:
> 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.

You've set up a system that isn't stable, but we don't have enough 
information to have any idea why. "I tried with new box size" doesn't go 
close to describing your method in enough detail for anyone to know 
where you went wrong.

See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for 
generic tips


> 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
>> MILES-IGERT Trainee
>> 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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