There can be many reasons for SCF convergence failure. Most likely your structure is too distorted. Make sure you are starting from a reasonable geometry. If you are running steered MD, then you may have pulled coordinates too quickly. You can add writepdb=1 to the &qmmm namelist to inspect coordinates in the QM region.
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 10:40 AM, Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu> wrote:
>
> 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
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>>>> 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
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Received on Mon Apr 17 2017 - 11:30:02 PDT
