Re: [AMBER] Single Point Energy: sander x python sander

From: Ray Luo <rluo.uci.edu> Date: Thu, 13 Jan 2022 09:06:18 -0800

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Thu, Jan 13, 2022 at 8:21 AM Alan <alanwilter.gmail.com> wrote:
> Thanks Prof. Case, please see the details below.
>
> On Thu, 13 Jan 2022 at 14:26, David A Case <david.case.rutgers.edu> wrote:
>
> > On Thu, Jan 13, 2022, Alan wrote:
> > >
> > >After reviewing Amber21 manual I updated to:
> > >cat << EOF >| mdin
> > >Single point
> > >&cntrl
> > >imin=0, maxcyc=0,
> > >ntmin=2,
> > >igb=6,
> > >//
> > >EOF
> >
> > Above looks suspicious: the default value for ntb is 1, and you don't
> reset
> > it to 0.  Study the mdout file to see if there is any evidence that you
> are
> > actually using PME.
> >
>
> I looked at the Amber21 manual.
> From 21.7.1. Generic parameters:
> It states igb > 0 implies ntb = 0 and cut = 9999.0
>
> from mdout:
> ntf     =       1, ntb     =       0, igb     =       6, nsnb    =      25
> dielc   =   1.00000, cut     =9999.00000, intdiel =   1.00000
>
> and no, not using PME.
>
> Using my old mdin (ntb=0, igb=0, cut=999) give the same result as the new
> one (igb=6).
> Also, when I compare with Gromacs I got the error inferior to 0.001% and
> I'm sure it's not using PME neither PBC.
>
>
> > >print(f"{inp.igb}, {inp.cut}, {inp.ntb}, {e.tot}, {e.elec}")
> >
> > As a check, compare the bond, angle and dihedral angles as well.
> >
>
> In details:
>                                  Python x    Sander
> error angle   :    0.48950 %    4.29874 x    4.27770
> error bond    :    2.04820 %    0.75717 x    0.77300
> error dihedral:    0.01374 %   14.90205 x   14.90410
> error vdw_14  :    0.04436 %    9.22471 x    9.22880
> error vdw     :    0.33978 %    3.83343 x    3.84650
> error elec_14 :    0.00867 %  231.30996 x  231.28990
> error elec    :    0.01118 % -263.32243 x -263.29300
> error tot     :    2.27586 %    1.00363 x    1.02700
>
> I'm still puzzle.
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