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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Received on Thu Jan 13 2022 - 08:30:02 PST
