[gmx-users] solvation_box_preparation

shahid nayeem msnayeem at gmail.com
Wed Feb 9 05:37:26 CET 2011 

Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy  = -3.9063050e+05
Maximum force     =  1.3442458e+02 on atom 927
Norm of force     =  1.4758101e+01
 For equilibration of solvation box I am following a biophys j paper
in which protocol for urea box preparation is given. A simulated
annealing under high pressure (ref_p=100) to cool system from 300 to
0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same
condition. If this way is harsh treatment of system then suggest me
the way out.
My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp
are attached with this mail
Shahid Nayeem
On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
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