[gmx-users] solvation_box_preparation
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 9 12:56:34 CET 2011
shahid nayeem wrote:
> 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
OK, so energy minimization was fine.
> 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
There's nothing obviously wrong with the .mdp file. Have you tried running
"normal" MD to check for stability? I suggested that before, and I'm still curious.
Also, your CHAPS topology makes no sense. The haphazard charge assignment and
nonsensical charge groups indicate to me that PRODRG has done its usual job of
assigning funny parameters. Even if you could get the simulations to run, they
shouldn't be trusted, and bad parameters could well be the source of your
problem. Parameterization is time-consuming and difficult, but so is generated
quality, usable data :)
-Justin
> 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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--
========================================
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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