[gmx-users] solvation_box_preparation

[Justin A. Lemkul]

shahid nayeem wrote:
> 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

PRODRG doesn't have a problem of missing charges.  It provides notoriously 
incorrect charges.

> 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

These settings make no sense.  An emtol of 2000 is very high, and emstep of 3000 
is total nonsense.  How well did you EM converge?  What were the values of the 
potential energy and maximum force?

> 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.

How about simplifying the problem.  Does the system run under normal conditions? 
  In other words, can you run normal MD?  You're treating the system very 
harshly with the combination of high pressure and annealing.  Without seeing 
your .mdp file for this process, it's impossible to say how reasonable your 
settings are.

It is also possible that your parameters for CHAPS (if they are the default ones 
from PRODRG) are incorrect.  The charges and charge groups nearly always are. 
Without seeing them, there's nothing better to offer.

-Justin

> 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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-- 
========================================

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

========================================