[gmx-users] Error energy minimization on protein with implicit water

[aiswarya pawar]

By setting the emtol to 1.0, didnt work. Anyother way i could figure out.

On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> lina wrote:
>
>> On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar <aiswarya.pawar at gmail.com>
>> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I have a MD simulated protein and i take frame from this and remove water
>>> and add water implicit in the interface and want to do energy
>>> minimization
>>> but while doing the minimization i get errors. The steps followed are-
>>>
>>> pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
>>> grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr
>>>
>>> The minim.mdp file =
>>>
>>> ; Lines starting with ';' ARE COMMENTS
>>> ; Everything following ';' is also comment
>>>
>>> title        = Energy Minimization    ; Title of run
>>>
>>> ; The following line tell the program the standard locations where to
>>> find
>>> certain files
>>> cpp        = /lib/cpp    ; Preprocessor
>>>
>>> ; Define can be used to control processes
>>> define          = -DFLEXIBLE
>>>
>>> ; Parameters describing what to do, when to stop and what to save
>>> integrator    = steep        ; Algorithm (steep = steepest descent
>>> minimization)
>>> emtol        = 1000.0    ; Stop minimization when the maximum force < 1.0
>>>
>> emtol = 1.0
>>
>
> If mdrun could not converge to 1000, setting a target of 1 will not solve
> anything.  The OP should refer to:
>
> http://www.gromacs.org/**Documentation/Errors#Stepsize_**
> too_small.2c_or_no_change_in_**energy._Converged_to_machine_**
> precision.2c_but_not_to_the_**requested_precision<http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision>
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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