Re: [AMBER] how to minimize with full electrostatics and no boundary conditions?

From: David A Case <>
Date: Tue, 31 Dec 2013 08:14:24 -0500

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
> 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


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Received on Tue Dec 31 2013 - 05:30:04 PST
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