BFEE2
BFEE2 copied to clipboard
fhh2626
binding free energy estimator 2
Is there a step-by-step tutorial for installing the BFEE2 VMD Plugin? I tried to install BFEE2 using conda on my Windows machine, but I am running into an issue. I...
NAMD 3.0
Hello, In your nature protocol paper did you use NAMD 3.0 GPU version to run the simulations? Did you use "CUDASOAintegrate on" in the input file which is required for...
I have tried to create simulation files using both BFEE and BFEE2 and no matter what whenever I run simulation on step 002_euler_theta I get the same error: ERROR: Constraint...
I get the following error when I use gromacs topology and pdb file 2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Initialization done. 2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Initialization done. 2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Setup the atoms group of the protein...
I downloaded the BFEE VMD plugin and was looking to perform binding calculations for a protein-protein system. I noticed that it does not let me select the protein:protein option and...
This commit add a dialog to collect the log, which can be triggered in the help menu. Also the format of logging in BFEEGromacs is improved to show the line...
we should use Parrinello-Rahman barostat in Gromacs, as Berendsen barostat is generally thought to be bad
Dear all, I'm experience the following mistakes: 1) I have prepared my system using charmm-gui (protein-ligand). when I run the equilibration step the target temperature is in average 309 K...
After alchemical analysis, when we perform Post-treatment, we provide .feout and .log files for calculating the binding energy, what values it takes from the .log file for calculating energy.
What is the distinction between the 'FEP' and 'BAR' estimation methods used in post-treatment alchemical analysis? Why are there two different calculation method provided, and which one is more effective...