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
