Jarzynski non-equilibrium simulations with Amber
Jarzynski non-equilibrium simulations are an alternative to FEP
calculations of free energies.
We have used it to calculate MM -> QM/MM free energies.
These are sample input files.
State 0 (MM)
NE simulation
&cntrl
irest=0,ntx=1,
nstlim=20000,dt=0.001,
temp0=300.0,ntt=3,gamma_ln=2.0,
ntc=2,ntf=1,
cut=8.0,
ntb=2,ntp=1,pres0=1.0,taup=1.0,
ntpr=100,ntwx=100,ntwv=100,ntwe=100,
icfe=1,clambda=0.000000,dynlmb=0.005,ntave=100,
ifmbar=1,
bar_intervall=100,bar_l_min=0.000,bar_l_max=1.000,bar_l_incr=0.005,
&end
State 1 (QM/MM)
NE simulation
&cntrl
irest=0,ntx=1,
nstlim=20000,dt=0.001,
temp0=300.0,ntt=3,gamma_ln=2.0,
ntc=2,ntf=1,
cut=8.0,
ntb=2,ntp=1,pres0=1.0,taup=1.0,
ntpr=100,ntwx=100,ntwv=100,ntwe=100,
icfe=1,clambda=0.000000,dynlmb=0.005,ntave=100,
ifmbar=1,
bar_intervall=100,bar_l_min=0.000,bar_l_max=1.000,bar_l_incr=0.005,
ifqnt=1,
/
&qmmm
qmmask=':1',
qmcharge=-1,
qm_theory='PM6-DH+',
/
The important parameters are
- number of independent simulations
- number of steps between changes in lambda (ntave)
- step of change in lambda (dynlmb)
The first determines the precision of the results.
The other two determine the length of the simulation.