Thanks for reply, Andy.
I tried both with constrains (ntc=2, ntf=2, qmshake=1) and without (ntc=1,
ntf=1, qmshake=0) and in both cases the overheating problem remained, but
the no-constrain option seems better. Changing the simulation step (60000
steps and dt=0.0001) helped a little bit, but the system is still heating
up very quickly to almost 400 K, while it should never go above 300 K. Over
next 30,000 steps the temperature goes down to around 300K and than
suddenly there's a huge temperature jump and the simulaton crashes (see the
log). Also there's no significant density change. Should I decrease the dt
even more untill the system is able to equilibrate properly?
NSTEP = 4550 TIME(PS) = 0.455 TEMP(K) = 399.18 PRESS =
645.9
Etot = -7690.4727 EKtot = 5712.5297 EPtot =
-13403.0023
BOND = 3055.9327 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
2867.4702
EELEC = -18777.5781 EHBOND = 0.0000 RESTRAINT =
0.0000
PM6ESCF= -548.8272
EKCMT = 1767.6945 VIRIAL = 822.2593 VOLUME =
67793.4301
Density =
0.7055
Ewald error estimate: 0.3479E-01
NSTEP = 29750 TIME(PS) = 2.975 TEMP(K) = 302.13 PRESS =
-356.2
Etot = 6120.6691 EKtot = 4323.6495 EPtot =
1797.0196
BOND = 18422.5094 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
2683.0628
EELEC = -18894.0653 EHBOND = 0.0000 RESTRAINT =
0.0000
PM6ESCF= -414.4873
EKCMT = 1408.0757 VIRIAL = 1909.1151 VOLUME =
65143.9360
Density =
0.7342
Ewald error estimate: 0.4139E-01
NSTEP = 29800 TIME(PS) = 2.980 TEMP(K) = 773.03 PRESS =
3992.6
Etot = 10842.6146 EKtot = 11062.5947 EPtot =
-219.9801
BOND = 16447.2282 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
2684.4291
EELEC = -18955.5385 EHBOND = 0.0000 RESTRAINT =
0.0000
PM6ESCF= -396.0989
EKCMT = 7641.9089 VIRIAL = 2026.1816 VOLUME =
65142.9022
Density =
0.7342
Ewald error estimate: 0.4170E-01
2017-08-08 23:58 GMT+02:00 Goetz, Andreas <agoetz.sdsc.edu>:
> Dear Artur,
>
> You constrain the geometry of MM water (ntc=2, ntf=2) but not for QM water
> (qmshake=0). This will lead to problems when water molecules exchange
> between the MM and QM regions. You either have to use a flexible water
> model or constrain the geometry of water both in the MM and in the QM
> region. Your heating procedure also looks aggressive but may work.
>
> I hope this helps,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Aug 8, 2017, at 2:03 PM, Artur Przydacz <
> artur.przydacz.dokt.p.lodz.pl> wrote:
> >
> > Dear Amber Users,
> >
> > I have a problem with adaptive QM/MM simulation. I have a quite simple
> > system, namely an amine solvated by water molecules I did minimisation,
> but
> > when I try to heat the system from 0K to 300K Amber doesn't stop at 300K
> > but keep heating it up untill the whole simulation crashes, which usually
> > happens at 600K using PM3 and at 400K using PM6. I am including the input
> > file and the groupfile, and if neccessary I will provide the output.
> >
> > Input:
> > Heating
> > &cntrl
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > nstlim = 20000,
> > dt = 0.001,
> > ntb = 2,
> > ntp = 1,
> > taup = 1.0,
> > cut = 8.0,
> > !ntr = 0,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0,
> > temp0 = 300.0,
> > ntt = 6,
> > gamma_ln = 5.0,
> > ntpr = 50,
> > ntwx = 1000,
> > ntwr = 5000,
> > ig=-1,
> > ifqnt=1
> > /
> > &qmmm
> > qmmask=':1',
> > qmcharge=0,
> > qm_theory='PM6',
> > adjust_q=0,
> > vsolv=2,
> > qmshake = 0,
> > qm_ewald = 1, qm_pme = 1,
> > verbosity = 0,
> > /
> > &vsolv
> > nearest_qm_solvent=8,
> > qm_center_atom_id=1,
> > verbosity = 1, debug = 0,
> > /
> > &adqmmm
> > n_partition=6,
> > verbosity=1,
> > print_qm_coords=1,
> > debug = 0, verbosity = 2,
> > /
> >
> > Groupfile:
> > # groupfile for adaptive solvent QM/MM run with n_partition = 6
> > -O -i heat.mdin -c min-IV.rst -p box-IV.prmtop -suffix heat
> > -O -i heat.mdin -c min-IV.rst -p box-IV.prmtop -suffix heat
> > -O -i heat.mdin -c min-IV.rst -p box-IV.prmtop -suffix heat
> > -O -i heat.mdin -c min-IV.rst -p box-IV.prmtop -suffix heat
> > -O -i heat.mdin -c min-IV.rst -p box-IV.prmtop -suffix heat
> > -O -i heat.mdin -c min-IV.rst -p box-IV.prmtop -r heat-IV.rst -x
> > heat-IV.mdcrd
> >
> > Best regards
> > Artur
> >
> > --
> > Institute of Organic Chemistry
> > Lodz University of Technology, Faculty of Chemistry
> > Żeromskiego 116, 90-924 Lodz, Poland
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Institute of Organic Chemistry
Lodz University of Technology, Faculty of Chemistry
Żeromskiego 116, 90-924 Lodz, Poland
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Received on Wed Aug 09 2017 - 05:30:02 PDT
