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
&end
END
END
Can you please let me know if you find something wrong with this input
file? My minimization is breaking the bonds :(
-Jose
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Received on Mon Dec 30 2013 - 12:00:02 PST
