Dear Brian,
thanks for your kind reply..
We did two step minimization process, heating in constant volume followed
by density equilibration under constant pressure. All these process were
performed only with classical md methodology. After a 500ps classical md
run QMMM was turned on. Two phase of 25ps QMMM simulations (with restart
after 25ps) ran without any problems. Extension of the second phase
resulted in the error. We observed some necessary conformational changes in
the structure without major disturbances. We are performing QMMM to observe
local changes only and not reaction mechanisms and hence SHAKE algorithm
was used.
On Tue, Aug 5, 2014 at 11:42 PM, Brian Radak <radak004.umn.edu> wrote:
> This could be due to a lot of things. The usual advice is to decrease your
> print step (*i.e.* set ntpr = ntwx = 1) and try to visualize what is
> happening up until the divergence occurs. Usually you will see a rather
> spectacular "explosion" of the QM region due to some specific event.
>
> Just glancing through your input you are turning of bond energies/forces
> with hydrogens via SHAKE, including in the QM region. I would strongly
> recommend setting "qmshake = 0". It is also rather perilous to do constant
> pressure MD with QM/MM unless your system density is stable. I'd recommend
> doing the density equilibration step with MM only or else with restraints
> on the quantum region.
>
> Regards,
> Brian
>
>
> On Tue, Aug 5, 2014 at 12:23 PM, Muthukumaran R <kumaran.bicpu.edu.in>
> wrote:
>
> > Dear amber users,
> > I am running QMMM module implemented in AMBER 12. Here is my md.in
> file.
> >
> > imin=0,irest=1,ntx=5,
> > nstlim=25000,dt=0.001,
> > ntc=2,ntf=2,
> > cut=10, ntb=2, ntp=1, taup=1.0,
> > ntpr=50, ntwx=50,
> > ntt=3, gamma_ln=2.0,
> > temp0=300.0,
> > ifqnt=1,
> > /
> > &qmmm
> > qmmask=":18-20,39-41,60-62",
> > qmcharge=-5,
> > qm_theory="PM3",
> > qmcut=10.0,
> > writepdb=1,
> > /
> >
> > After running simulation for 50ps, while extending it to further time
> > period ends in following error..
> >
> > QMMM: WARNING!
> > QMMM: Unable to achieve self consistency to the tolerances specified
> > QMMM: No convergence in SCF after 1000 steps.
> > QMMM: Job will continue with unconverged SCF. Warning energies
> > QMMM: and forces for this step will not be accurate.
> > QMMM: E = -0.1349E+08 DeltaE = -0.2833E+05 DeltaP = 0.1770E+01
> > QMMM: Smallest DeltaE = 0.2069E+03 DeltaP = 0.1570E+01 Step = 73
> >
> > How to solve this error??
> >
> > Thanks in advance..
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for
> Integrative Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
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Received on Tue Aug 05 2014 - 22:00:02 PDT
