Hello Amber users,
I have some questions while repeating the thermodynamic integration in tutorial 9.
1. First in newer version of tutorial 9, during the pre-TI equilibration of ligand and complex system in water, the solute molecules are applied restraints. But in older version of tutorial, there were no restraints. Why is it better to keep protein and ligands static during simulation?
2. In the output of TI integration, there are outcomes for both TI region 1 and TI region 2. I noticed that only in the second state where benzene is pertuated into phenol that involves use of soft core vdw potential, the total energy are different for TI region 1 and TI region 2. BUt, during decharging and recharging process, every term of energy are same for every step and all lamda values. Why is that and what do TI region 1 and TI region 2 represent? For instance,If benzene is in the process of decharging and TI region 1 and 2 represent the state of charged and partialled/totally decharged respectively , at least electrostatic energy should be different for TI region 1 and TI region 2.
3. According to the manual, when calculating the free energy change, dV/dlamda should multiply to weights that depends on value of lamda, but in script getdvdl.py, integration does not involve in any weight value. Is it a mistake?
4 When collecting dV/dlamda values for integration, should I average dV/dlamda for all steps or just few steps before simulation finished, or just dV/dlamda of last step?
2. In the input of TI integraion, for each simulation of lamda value, ifmbar = 1,mbar_states = 11 , mbar_lambda = 0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, does these three commands affect calculation of dV/dlamda for each simulation of a specific lamda value?
Best,
Thanks,
Xiang
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Received on Sat Jan 08 2022 - 08:30:02 PST
