I guess I'll do that! I am already having lots of issues with my current
SMD run! Amber14 works but the simulation now is giving me this error:
QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
QMMM SCC-DFTB: Convergence could not be achieved in this step.
QMMM SCC-DFTB: The calculation will continue, but energies and
QMMM SCC-DFTB: forces for this step will not be accurate.
I think I need to go back and check my QMMM equilibration again before
running SMD. Unfortunately the Amber tutorial on SMD (
http://ambermd.org/tutorials/advanced/tutorial10/) does not provide much of
information regarding the initial distance RST file, I used makeDIST to
generate distance between N atom on a lysine and O of a water molecule on
my weird system! (
http://archive.ambermd.org/201704/0114.html) but makeDIST
generated a group restraint of 3 H atoms attached to N on Lysine (-NH3+)
and the oxygen atom on water.
#
# 12 LYS NZ 23 WAT O 1.30 3.50
&rst
ixpk= 0, nxpk= 0, iat= -1, 270, r1= 0.80, r2= 1.30, r3= 4.20, r4= 4.70,
rk2=20.0, rk3=1000.0, ir6=1, ialtd=0,
igr1= 140, 141, 142,
/
I run two equilibration simulations: one with the RST between O and H
atoms as single group (igr1) and the second one between N atom and O. The
one from the group atoms seemed OK but the N and O equilibration lead to
strange behaviour and as I visualized it, the bond length between N and H
was increasing like crazy! So I got my replicates for SMD from the
equilibration of O atom and H-group restraints. However the path on SMD run
monitors the proton transfer from N to O and has nothing to do with my atom
selection for the equilibration!
Will try to solve this problem first and then move to fixing update
issues. Thank you so much for all your wonderful help!
Best,
Sam
On Thu, Apr 13, 2017 at 12:35 PM, Hannes Loeffler <
Hannes.Loeffler.stfc.ac.uk> wrote:
> I am not sure what your problem there is but my suggestions would be to
> do a fresh download of the AmberTools and then start the update process
> with the Python tool. But since AmberTools17 are soon to be released
> you may want to just wait for that.
>
> Cheers,
> Hannes.
>
>
> On Thu, 13 Apr 2017 12:01:35 -0400
> Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
>
> > Thank you for your fast reply. I remember now, this is update.9! I was
> > getting an error like this one
> > (http://archive.ambermd.org/201610/0212.html) when I was updating
> > before installation and couldn't solve it. Reading through update 4
> > and 9 description at the time (way before my need for nscu!), I
> > decided to continue without. I will use Amber14 for this particular
> > run now but I need to fix the problem for future runs, update and
> > recompile. I would greatly appreciate if you have any suggestion on
> > how to fix this update issue. Sincerely yours,
> > Sam
> >
> > On Thu, Apr 13, 2017 at 11:40 AM, Hannes Loeffler <
> > Hannes.Loeffler.stfc.ac.uk> wrote:
> >
> > > On Thu, 13 Apr 2017 11:29:59 -0400
> > > Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
> > >
> > > > Dear Amber Users and Developers
> > > > I am trying to perform a QMMM SMD simulation to monitor a PT
> > > > reaction. I equilibrated my system and obtained replicates,
> > > > However when I subject the replicates to SMD using the fallowing
> > > > parameters and sander.MPI, it seems like sander is not reading
> > > > the ncsu section and the variables.
> > >
> > > I suppose you have applied the recent updates to AmberTools. The
> > > code (now called NFE) has been changed to read all inputs through
> > > namelists. See nfe.pdf on http://ambermd.org/bugfixesat.html .
> > >
> > >
> > > Cheers,
> > > Hannes.
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
>
>
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>
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Thu Apr 13 2017 - 10:00:03 PDT
