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

[Justin A. Lemkul]

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

-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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