[gmx-users] solvation_box_preparation

[shahid nayeem]

Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box
with genbox inserting 7 molecules of chaps.gro. Then again using
genbox and -maxsol I put 510 spc.itp in the box to get a density
approaching 1. Then I did steepest descent energy minimization with
constraints = none, for emtotal=2000 and emstep=3000. Up to this the
gromacs runs fine. when I start simulated annealing for cooling at
high pressure with constraint = all_bonds the programme gives fatal
error linc warning and stops. If I do energy minimization with
constraint =all_bonds then also with some error of linc wrning the
minimization is completed. When I do minimization without adding water
then there is no linc warning and minimization is completed but with
final positive potential energy. Then as suggested by Justin I used
smaller box and there also in simulated annealing stage the system
gives linc warning and the programme stops with fatal error. Please
tell me where I am wrong.
shahid nayeem

On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
>
> Mark
>
>> 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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