I tried to equilibrate the system using the same QMMM parameters with
distance restraints on H-donor and acceptor and determined the CV value.
when I subjected to SMD at DFTB and sampled the trajectory with ( ntpr =
1, ntwr=1, ntwx = 1,), after a while the stsyem blows up in the QM region.
I tried different CV values, turned off the SHAKE even in MM calculations
(in QM it is always off), changed the harm value, QM level from DFTB to
PM3, nothing can fix it! The initial structure looks reasonable. Here is a
an example of the mdin and cv.in as well as prmtop and rst files:
LYS12H2O: PT using NCSU steered MD with LCOD rxn coord
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 0,
cut = 999.0,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
ntf = 2, ntc = 2, tol = 0.00001,
dt = 0.0005,
ntpr = 1, ntwr=1, ntwx = 1,
nstlim = 100000,
infe = 1,
ifqnt = 1,
/
&qmmm
qmmask=':12, 23 ', !QM region mask LYS 12 and a SINGLE WATER
qmcharge=1, !QM region charge, not total system
qm_theory='DFTB',
qmshake=0,
writepdb=1,
/
&smd
output_file = 'work.txt'
output_freq = 10
cv_file = 'cv.in'
/
the cv.in file:
&colvar
cv_type ='LCOD',
cv_i = 139, 141, 270, 141,
cv_r = 1.0, -1.0,
cv_ni = 4, cv_nr= 2,
path = 3.5, -3.5,
npath = 2,
harm = 100.0,
nharm = 1,
/
Best,
Sam
On Mon, Apr 17, 2017 at 2:21 PM, Goetz, Andreas <agoetz.sdsc.edu> wrote:
> 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
> >>>> 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 - 12:00:02 PDT
