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>
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Received on Mon Apr 17 2017 - 10:30:03 PDT
