[gmx-users] Energy minimization has stopped

Thu Jun 23 13:23:26 CEST 2016

Hi,

You were recommended to pick a force field, not to combine parts of force
fields. Choosing to simulate your polymer OPLS/AA if you then want to
combine with RNA is not a good experimental design, unless you can do the
combined simulation also in OPLS/AA. I would repeat the polymer experiment
in whatever forcefield is also good for the experiment with RNA.

Mark

On Thu, Jun 23, 2016 at 1:18 PM Anurag Dobhal <
anurag.dobhal at nano-medicine.co.in> wrote:

> 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
> >
> > ==================================================
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