Thank you so much Andy and Feng. Will stick to sander then!
Best,
Sam
On Mon, Apr 17, 2017 at 1:15 PM, Goetz, Andreas <agoetz.sdsc.edu> wrote:
> Hi Sam,
>
> You are right: QM/MM is only available in sander, not pmemd. Since QM is
> the bottleneck, there is no reason to port this functionality over to pmemd.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Apr 17, 2017, at 9:50 AM, Samaneh Ghassabi Kondalaji <
> saghassabikondalaji.mix.wvu.edu> wrote:
> >
> > Update after fixing all errors:
> > As it turns out, I had fixed the update 4 and 9 errors before! The
> > $AMBERHOME/update_amber --show-unapplied-patches does not return any
> value
> > for unapplied patches. I don't remember exactly but I assume the error
> was
> > gone after I solved the issue I had with my Python version.
> > I can use the NFE toolkit on both sander and pmemd to do steered MD
> > simulations, however as I remember, the pmemd could not perform any QMMM
> > runs (there is a &qmmm in my mdin file). Is this still the case in
> Amber16?
> > Best,
> > Sam
> >
> > On Thu, Apr 13, 2017 at 12:56 PM, Samaneh Ghassabi Kondalaji <
> > saghassabikondalaji.mix.wvu.edu> wrote:
> >
> >> 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
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> *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>
> >>
> >>
> >
> >
> >
> > --
> > *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>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*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 Mon Apr 17 2017 - 10:30:04 PDT
