[AMBER] adaptive qm/mm NVT not reaching target temperature

From: Stanislav Simko <s.simko.uu.nl>
Date: Wed, 25 May 2016 14:58:39 +0200

Dear all,
we're running the adaptive qm/mm NVT equilibration with the target
temperature 300K (default temperature). However, we're reaching
temperatures up to 280K. 
Our QM/MM region is fairly small - up to 4.5A sphere in the 40A box,
with several transition regions - 0.3, 0.5, 0.75, 1.0 and 1.25
Angstrom, so there's up to ~10 H2O molecules in the QM/MM. Therefore,
the effect on the temperature should be negligible. 
We're getting the same effect as show on the the attached files for the
0.75A case for all of the simulations. 

At first we ran full MM NPT and then NVT equilibration and used the
final restart as input for each of the QM/MM calculations. Very strange
is also that the temperature drops by 100K already after the first
step. 
Please, do you have any suggestions what could be going wrong? 
Attached are our input file for the 0.75A case and its temperature plot
and the temperature plot for the NVT equilibration
Thank you very much.
Regards 
stanislav.


adaptive QM/MM (A/T region defined by radii), NVE dynamics for 100 steps at dt=0.5fs
 &cntrl
  imin = 0, ! do MD (no minimization)
  irest = 1, ! trajectory restart
  ntx = 5, ! read coordinates and velocities
  dt = 0.0005 ! 0.5fs time step
  ntb = 1, ! periodic boundary conditions
  ntt = 3, ! Langevin thermostat
  gamma_ln = 0.1, ! Collision frequency
  cut = 8.0, ! non-bonded cutoff
  ntpr = 1, ! logfile print frequency
  ntwx = 1, ! coordinate writing frequency
  ntwr = 10, ! restart file writing frequency
  nstlim = 20000, ! number of steps
  jfastw = 4, ! do not use routines for fast triangulated water
  iwrap = 1, ! wrap periodic molecules back into box
  ifqnt = 1, ! QMMM
 /
 &ewald
  dsum_tol = 0.000001, ! Increase PME accuracy
 /
 &qmmm
  qmmask = ':339',
  qm_theory = 'EXTERN',
  scfconv = 1.0d-8,
  tight_p_conv = 0,
  vsolv = 3, ! adQMMM with fixed RA and RT
  adjust_q = 0, ! required for vsolv
  qmcharge=0,
  spin=1,
  qmcut=14,
  qm_ewald=0,
  qmmm_switch=1,
  r_switch_hi=14,
  r_switch_lo=12,
  writepdb=1,
 /
 &vsolv
  nearest_qm_solvent = 2, ! solvent in active region
  nearest_qm_solvent_resname = 'WAT', ! solvent resname
  nearest_qm_solvent_fq = 1, ! every step
  nearest_qm_solvent_center_id = 0, ! number of atom in solvent residue defining solvent center
  qm_center_atom_id = 1015, ! absolute number of atom defining QM center
  verbosity = 1,
  debug = 0,
 /
 &adqmmm
  n_partition = 14, ! (n-1) molecules in T region
  RA = 3.00,
  RT = 3.75,
  calc_wbk = 2, ! calculate energy correction
  verbosity = 3,
  print_qm_coords = 0,
 /
 &orc
  use_template=1,
 /


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Received on Wed May 25 2016 - 06:00:04 PDT
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