Thanks for the suggestion. I also realized I wasn't doing any steepest
descent at the very beginning. I changed this, and also set the neighbour
list to update every step, just in case. The minimization went well after
these changes!
On Tue, Dec 31, 2013 at 8:14 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Dec 30, 2013, Jose Borreguero wrote:
> >
> > 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
> > &end
> > END
> > END
> >
> > Can you please let me know if you find something wrong with this input
> > file? My minimization is breaking the bonds :(
>
> You input looks OK. What is it that make you think bonds are being broken?
> That is (nearly) impossible with a molecular mechanics force field.
>
> Set maxcyc to 20 and ntpr to 1: look carefully at the energies and the
> final
> structure.
>
> ...dac
>
>
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Received on Tue Dec 31 2013 - 11:30:02 PST
