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

From: Jose Borreguero <borreguero.gmail.com>
Date: Mon, 30 Dec 2013 14:36:15 -0500

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
   imin=1, ntmin=0, !invoke full conjugate gradient minimization for X
   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
   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

Can you please let me know if you find something wrong with this input
file? My minimization is breaking the bonds :(

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Received on Mon Dec 30 2013 - 12:00:02 PST
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