Hi Artur,
The temperature increase at the beginning of the simulation is expected, assuming that you start from some MM geometry. In this case your system is far from equilibrium, which may lead to large forces when switching from an MM to a QM potential. The temperature jump at the end of the simulation should not happen. If you want you can send me input files (mdin, inpcrd, prmtop) directly by email or share in some other way, and I will try to have a look.
All the best,
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 9, 2017, at 5:28 AM, Artur Przydacz <artur.przydacz.dokt.p.lodz.pl> wrote:
>
> 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
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>>> 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 Thu Aug 10 2017 - 01:00:02 PDT
