[AMBER] QM/MM energy minimization

From: Stanislav Simko <s.simko.uu.nl>
Date: Fri, 20 May 2016 12:34:28 +0200

Dear all,
i'm having a strange problem with QM (/MM) system. I have 2 water
molecules that are, for now, QM and zero MM molecules. Later on I want
to change one of them to MM and add more water molecules that should be
QM/MM (adaptive). I'm using ORCA for the QM part of the calculation.
The problem is however, that the QM input coordinates are not being
updated - ORCA is working all the time with the original structure, but
Amber not. Do you please have got any suggestions where am i doing a
mistake?.
Thank you.
Sincerely,
stanislav.
my inputs (parameter file is attached):

Energy minimisation of fully QM Water Dimer
 &cntrl
  imin=1,       ! Perform an energy minimization
  ntx=1,        ! Read coordinates but not velocities from inpcrd file
  irest=0,      ! Do not restart the simulation
  ntpr=1,       ! Logfile print frequency
  ntwr=1,       ! Restart file writing frequency
  maxcyc=200,   ! Maximum minimisation cycles
  ntmin=0,      ! For ncyc cycles steepest descent method is used then
conjugate gradient is switched on
  ntc=1,        ! SHAKE is not performed
  jfastw=4,     ! Do not use fast SHAKE routines for water
  ntf=1,        ! Complete interaction is calculated
  ntb=0,        ! No periodicity is applied and PME is off
  cut=20.0,      ! Nonbonded cutoff
  igb=0,        ! No generalized Born term is used
  ifqnt=1,      ! Include &qmmm namelist
 /
 &qmmm
  qmmask=':1-2',        ! Residues 1 and 2 are quantum
  qm_theory='EXTERN',   ! Use external programme for QM theory (orca)
  scfconv=1.0d-8,       ! Convergence criteria in kcal/mol
  tight_p_conv=0,       ! Loose convergence on the density matrix
  vsolv=0,              ! Do not include solvent molecules in QM region
  adjust_q=0,           ! No adjustment of charge is done
  qmcharge=0,           ! Total charge of qm atom list defined in
qmmask
  spin=1,               ! Multiplicity of the QM system
  qmcut=20,
  qm_ewald=0,           ! Real-space cutoff for QM-QM and QM-MM longe
range interactions
  qmmm_switch=0,
  r_switch_hi=14,
  r_switch_lo=12,
  writepdb=1,
 /
 &orc
  method = 'PBE',
  basis = '3-21G',
  use_template = 1,
 /

###################################################################
orc_job.tpl:
# ORCA input file
%pal nprocs 1 end
!PBE 3-21G verytightscf
%BASIS GTOAUX=AutoBuild END
%method
  grid 4
  finalgrid 6
end
%scf
  maxiter 100
end
%MaxCore 1024
! Angs NoUseSym


##################################################################
input structure:
default
    6
   1.9677787   3.3749857   1.8014289   1.1016907   2.8590060   1.819734
2
   2.4542947   3.0348384   2.6339204   3.7215928   1.6446749   2.451509
9
   3.2544504   2.0392279   1.6286084   4.6361695   2.0600117   2.426623
2
   50.953000   50.356000   50.893000  90.0000000  90.0000000  90.000000
0

-- 
Stanislav Simko.
PhD applicant
Inorganic Chemistry and Catalysis



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Received on Fri May 20 2016 - 04:00:04 PDT
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