121
Keep complex fixed
10.0
RES 1 15
END
END
/
Keep complex fixed
10.0
RES 1 15
END
END
5. Input files for density equilibration with AMBER:
Density.in
Molecular Dynamics on whole system
&cntrl
imin=0, irest=1, cut=10.0,
ntb=2, pres0=1.0, Constant pressure
ntp=1, taup=2.0, Pressure relaxation time (in
ps)
ntc=2, ntf=2,
tempi=310.0, temp0=310.0, ntt=3, gamma_ln=2.0,
nstlim=200000, dt=0.002,
/
Keep complex fixed
10.0
RES 1 15
END
END
Eq.in
Molecular Dynamics on whole system
&cntrl
imin=0, irest=1,
cut=10.0, ntb=2, pres0=1.0, ntp=1, taup=2.0,
ntr=0,
ntc=2, ntf=2,
tempi=310.0, temp0=310.0,
ntt=3, gamma_ln=2.0,
nstlim=200000, dt=0.002,
/end
6. Input file for production MD run with AMBER:
MD.in
Molecular Dynamics on whole system for 3 μs
&cntrl
imin=0, irest=1,
Molecular Dynamics and Drug Complexation with Cyclodextrins