Haohao Fu

> Hi Haohao, The NAMD implementation still needs some refinement: it comes with performance limitations, namely, you cannot use MTS and you need energy computation every time step. Other than...

Thanks for your clarification!

Hi, @jhenin , I suggest also make available the Colvars harmonic restraints as the alchemical CVs, which will let us completely give up FEP/TI in binding free energy calculations. Haohao

currently, it takes: ``` colvars: Lambda= 1 dA/dLambda= 0.995394 colvars: Lambda= 0.9999 dA/dLambda= 0.827822 colvars: Lambda= 0.999 dA/dLambda= 0.760705 colvars: Lambda= 0.99 dA/dLambda= 0.800472 ```

For complex cases, the stratification strategy reduce the probability of out-of-eqilibrium motion, and therefore improving the convergence rate. Usually I use 5 windows for the separation step. If the ligand...

You can restart the simulation using the .restart.coor, .restart.vel, .restart.xsc files. You need to know from which window the simulation restarts. Then change the `runFEP ...` line of the config...

You can have a look at gui.py (lines 1382-2021) to see how to call the internal APIs.

The fepout files have sections starting with `#NEW FEP WINDOW: LAMBDA SET TO aaa LAMBDA2 bbb` and end with `#Free energy change for lambda window [ aaa bbb ] is...

1. I am not sure, but the error seems OK. 2. You can always turn to the Bussi thermostat if you want.

I don't think there is an obvious limitation with the bussi thermostat