I got one more question! Do you have any suggestions why I am getting 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.
Best Regards,
Sam
On Mon, Apr 17, 2017 at 1:19 PM, Samaneh Ghassabi Kondalaji <
saghassabikondalaji.mix.wvu.edu> wrote:
> 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>
>
>
--
*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 - 11:00:02 PDT
