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 <jalem...@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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