[gmx-users] Energy minimization has stopped

[Anurag Dobhal]

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>
>>
>>
>> On 6/23/16 6:35 AM, Anurag Dobhal wrote:
>>
>>> Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
>>> field. I have written parameters using CHARMM27 force field for RNA
>>> molecules.
>>>
>>>
>> What does this mean?  Are you using OPLS-AA or CHARMM27?
>>
>>
> Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> superior for RNA.
>
> -Justin
>
>
> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>
>>> Energy minimization has stopped, but the forces have not converged to the
>>> requested precision Fmax < 1000 (which may not be possible for your
>>> system).
>>> It stopped because the algorithm tried to make a new step whose size was
>>> too
>>> small, or there was no change in the energy since last step. Either way,
>>> we
>>> regard the minimization as converged to within the available machine
>>> precision, given your starting configuration and EM parameters.
>>>
>>> Double precision normally gives you higher accuracy, but this is often
>>> not
>>> needed for preparing to run molecular dynamics.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints altogether (set constraints = none in mdp file)
>>>
>>>
>>> -----------------------------------------------------------------------------------------------------
>>>
>>> The contents of the .mdp file are the following
>>>
>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>>> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
>>> kJ/mol/nm
>>> emstep      = 0.01      ; Energy step size
>>> nsteps = 50000   ; Maximum number of (minimization) steps to perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to
>>> calculate the interactions
>>> nstlist    = 1    ; Frequency to update the neighbor list and long range
>>> forces
>>> cutoff-scheme   = Verlet
>>> ns_type    = grid ; Method to determine neighbor list (simple, grid)
>>> coulombtype    = PME ; Treatment of long range electrostatic interactions
>>> rcoulomb    = 1.0 ; Short-range electrostatic cut-off
>>> rvdw    = 1.0 ; Short-range Van der Waals cut-off
>>> pbc        = xyz ; Periodic Boundary Conditions (yes/no)
>>>
>>> any suggestions ?
>>>
>>>
>>
>> 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
>>
>>
>> mdrun prints which atom is feeling the maximum force, so that's a good
>> place to
>> start looking to see if there is an actual problem.
>>
>> -Justin
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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