Dear AMBER users,
I'm running an NPT QM/MM simulation using the AMBER/ORCA interface using PBE for the QM system. The system is composed of a nucleosde (QM) dissolved in a 20 A water box (MM).The system is equilibrated in the NPT ensemble classically and using also DFTB as implemented in AMBER. I'm using spcfw water model and 0.5 fs time step and no shake..I'm noticing that the dipole moment of the QM region is lowered by time and also the system density. At the first period the dipole moment is more than (10 D) which as i understand a result for the presence of the water molecules which increases the dipole moment. Afterthat, after around 2000 timesteps (almost 1 ps) the dipole moment is decreased and also the density. Density drops from (1.0097 to 0.9929 ), also the volume increase a little bit (104011.5218 to ====> 105806.9653). i visualized the trajectory and i didn't find anything problematic. Could you please comment.
I'm using periodic boundary conditions. I'm allowing the water molecules flexibility..Below is the input.
Regards
Marawan
system equilibration qm-mm
&cntrl
imin = 0,
ntpr = 1,ntwx = 1, ntwr = 1000,
nstlim = 6000,dt = 0.0005,
tempi = 300.0, temp0 = 300.0,
ntb=2, ntp=1, taup=1,
ntr = 0,
cut = 15.0, ig=-1,jfastw=4,
ntt = 3, gamma_ln = 10.0, ifqnt=1
&end
&qmmm
qmmask=':1'
qmcharge=0,
qm_theory='EXTERN',
qmcut=15.0,
qm_ewald=0
&end
&orc
use_template=1,
ntpr=1,
num_threads=8,
dipole=1
&end
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Received on Mon Dec 03 2012 - 01:30:02 PST
