On Mon, Dec 30, 2013 at 2:36 PM, Jose Borreguero <borreguero.gmail.com>wrote:
> Dear AMBER users,
>
> I have the following input file intended for minimization of a small
> molecule in vacuum. I want to do the minimization with full electrostatics
> but without the Ewald summation, and no boundary conditions. The molecule
> is small enough so that the electrostatics cutoff (12A) encompasses the
> whole molecule.
>
> Minimization with sander, no boundary conditions
> &cntrl
> imin=1, ntmin=0, !invoke full conjugate gradient minimization for X
> steps
> maxcyc=20000, !minimization for X steps (20000 is a good value)
> nsnb=5, !update of pair list frequency, 25 at equilibrium
> cut=12.0, !electrostatics cutoff
> ntc=1, !SHAKE flag, 1:no shake, 2: shake hydrogens, 3: shake all
> bonds
> ntf=1, !force evaluation, tipically ntf=ntc, 1:complete,
> 2:no-bonds-with-H, 3:no-bonded
> ntb=0, !periodic-bound-cond, 0:no 1:yes
> ntpr=20, !output energy information to mdout and mdinfo
> ntwx=100, !output coordinates to mdcrd
> ntwe=20, !output energies and temperatures to mden
> ntwr=2000, !output restart file
>
Try setting igb=6. That option gives gas-phase energies.
> &end
> END
> END
>
> Can you please let me know if you find something wrong with this input
> file? My minimization is breaking the bonds :(
>
Minimization should not break bonds. It could be that bonds that you think
are present are not present or that the force constant is too weak. You
can inspect your topology file with ParmEd and use various print* commands
(like printBonds, printAngles, etc.) to print out details about the
parameters.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 30 2013 - 13:00:02 PST
