Brandon Havranek

NAMD 3.0

2

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...

ERROR: Constraint failure in RATTLE algorithm for atom 2572!

3

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...

BFEE VMD Plugin

2

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...