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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Received on Tue Aug 08 2017 - 15:00:02 PDT
