[gmx-users] Energy minimization has stopped

[Justin Lemkul]

On 6/23/16 7:00 AM, Anurag Dobhal wrote:
> I am using OPLS AA force field. parameters (charges) for the atoms are
> taken from the charmm27 force field.
>

So, by using some hybridized force field, you can't successfully minimize a 
structure.  That should tell you something.  Why are you trying to do this, and 
what leads you to believe that some hybrid OPLS/CHARMM combination is even 
sensible?  You can't just mix the charges from one force field with another to 
create some kind of Frankenforcefield.

Recent RNA force fields like CHARMM36 and recent AMBER updates are highly 
optimized for RNA simulations.

-Justin

>
>
>
> *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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>

-- 
==================================================

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

==================================================