[gmx-users] error during energy minimization

[Itamar Kass]

    This is normal behavior, you can start your positional restrain MD.   
For further discussion on this subject, search the GROMACS site.
          Kass.

On Feb 22, 2005, at 2:01 PM, shailza singh wrote:

>
>
> dear Itamar,
> I used the following parameters for my protein :
>
> title                    = Yo
> cpp                      = /lib/cpp
> include                  = -I../top
> define                   = -DFLEX_SPC
> integrator               = steep
> nsteps                   = 50000
> emtol                    = 500.0
> emstep                   = 0.001
>
>
> and received the following output:
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 500
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy,
> or turn
> off constraints alltogether (set constraints = none in
> mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 38
> steps,
> but did not reach the requested Fmax < 500.
> Potential Energy  = -3.6378316e+05
> Maximum force     =  2.7210256e+03 on atom 25146
> Norm of force     =  1.7527736e+05
>
> what does this Fmax < 500 means?I think the criterium
> is also not set for the next step as Potential energy
> should be:Potential Energy  = -1.19482e+05(online
> reference)
>
> Please help as I have performed this a number of times
> but not being able to perform MD run.
> thanking you in advance
> shailza.
>
>
>
>
>  --- Itamar Kass <ikass at cc.huji.ac.il> wrote:
>>
>> On Feb 22, 2005, at 12:07 PM, shailza singh wrote:
>>
>>>
>>> Dear Itamar,
>>> I have one query... i am doing energy minimization
>> of
>>> the peptide in solvent..for that I followed the
>> steps
>>> as that given in getting-started Peptide in the
>>> GROMACS  online reference.The em.mdp file (sample
>> file
>>> given in the online reference) has integrator as
>> md
>>> ...do I need to change it as cg?What I did was
>> first
>>> perform energy minimization of the peptide in
>>> solvent..then short MD run and finally full MD
>> run.Am
>>> I proceeding in the right direction?or Do i need
>> to
>>> change the integator as cg?
>>>
>>
>> Hi shailza, the steps you stated seems fine to me,
>> but I am working on
>> in membrane peptide. Any how, in order to do EM you
>> should use cg
>> integrator.  For example:
>> define              =  -DFLEX_SPC
>> integrator           =  cg
>> nsteps               =  50000
>> ;       Energy minimizing stuff
>> emtol                =  500.0
>> emstep               =  0.001
>>
>> Later on, you should do short MD run in which the
>> peptide atoms are
>> restrained, for example:
>> integrator           =  md
>> dt                   =  0.002	; ps !
>> nsteps               =  250000	; total 0.5s.
>> ; Constrain control
>> define               = -DPOSRES
>> constraints          = all-bonds
>> The flag -DPOSRES indicate you use the position
>> restrains given in the
>> itp file (e.g. posre_A.itp) created by pdb2gmx.
>> Later on run a longer
>> simulation without position restrains.
>>
>>> My second question is :I changed both the
>> temperature
>>> coupling and pressure coupling ...and I got
>>> step 960, will finish at Tue Feb 22 16:46:00
>>> 2005Warning: 1-4 interaction between 1528 and 1533
>> at
>>> distance larger than 1 nm
>>> These are ignored for the rest of the simulation
>>> turn on -debug for more information
>>>
>>> Step 961, time 1.922 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> max 0.019805 (between atoms 1531 and 1532) rms
>>> 0.000548
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current,
>> constraint
>>> length
>>>    1531   1532   51.8    0.9733   0.0980
>> 0.1000
>>>
>>> Step 962, time 1.924 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> max 3.965767 (between atoms 1531 and 1532) rms
>>> 0.106540
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current,
>> constraint
>>> length
>>>    1531   1532   90.0    0.0980   0.4966
>> 0.1000
>>>    1531   1533   90.0    0.0996   0.4604
>> 0.1000
>>> After this its running fine.
>>> Please tell me as to where am i doing wrong?
>>> thanking you in advance
>>> shailza.
>>>
>>
>> This is probably due to some defect in your starting
>> structure, maybe a
>> collision between atoms or like.  If it ends fine it
>> O.K..  Again, what
>> you did was MD and not EM, I guess that doing EM
>> first will prevent
>> this kind of problems.
>>
>>
>>       Good luck, Itamar.
>>
>>
>> ===========================================
>> | Itamar Kass
>> | The Alexander Silberman
>> | Institute of Life Sciences
>> | Department of Biological Chemistry
>> | The Hebrew University, Givat-Ram
>> | Jerusalem, 91904, Israel
>> | Tel: +972-(0)2-6585194
>> | Fax: +972-(0)2-6584329
>> | Email: ikass at cc.huji.ac.il
>> | Homepage:
>>
> http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
>> ============================================
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