Free energy calculations of Hydan

Data structure

Simulations	Folders	Scripts	Tapes
Hydan endpoint	/home/xie/charmm/gp/hydan/	dynamics.inp	071099.list
Me-Hydan endpoint	/home/xie/charmm/gp/mhydan/	dynamics.inp	071099.list
N-Hydan endpoint	/home/xie/charmm/gp/nhydan/	dynamics.inp	071099.list
O-Hydan endpoint	/home/xie/charmm/gp/ohydan/	dynamics.inp	071099.list
Hydan in water	/home/xie/charmm/gp/whydan/	dynamics.inp	071099.list
Me-Hydan in water	/home/xie/charmm/gp/wmhyda/	dynamics.inp	071099.list
N-Hydan in water	/home/xie/charmm/gp/wnhyda/	dynamics.inp	071099.list
O-Hydan in water	/home/xie/charmm/gp/wohyda/	dynamics.inp	071099.list
Hydan0 Hydan	/home/xie/charmm/gp/hydan0/	dynamics.back.inp	061100.list
HydanMe-hydan	/home/xie/charmm/gp/hmdan/	dynamics.inp*	231100.list
Me-HydanHydan	/home/xie/charmm/gp/mhdan/	dynamics.inp*	241100.list
HydanN-Hydan	/home/xie/charmm/gp/hndan/	dynamics.inp	221099.list
Hydan0N-Hydan	/home/xie/charmm/gp/hndan0/	dynamics.inp	261000.list
N-HydanHydan0	/home/xie/charmm/gp/nhdan0/	dynamics.inp	201099.list
Me-Hydan N-Hydan	/home/xie/charmm/gp/mndan/	dynamics.inp	090699.list 220699.list
N-HydanO-Hydan	/home/xie/charmm/gp/nodan/	dynamics.inp	051099.list
O-HydanN-Hydan	/home/xie/charmm/gp/ondan/	dynamics.inp
HydanO-Hydan	/home/xie/charmm/gp/hodan/	dynamics.inp	041099.list 090899.list
O-HydanHydan	/home/xie/charmm/gp/ohdan/	dynamics.back.inp	060799.list 080899.list
Hydan0O-Hydan	/home/xie/charmm/gp/hodan0/	dynamics.inp
HydanO-Hydan in water	/home/xie/charmm/gp/whodan/	dynamics_solution.inp	210699.list
Me-HydanN-Hydan in water			260599.list

Result summary

Slow growth method

Polynormial path method

• Conventional thermodynamical integration method: The main script for Hydan to Me-Hydan conversion.
• Combined slow growth and polynormial path method: The main script for Hydan to Me-Hydan conversion.