[gmx-users] Energy minimization has stopped

Thu Jun 23 13:17:37 CEST 2016

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.

Thank You

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

On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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