Pick one frame from namd dcd file and save it to another single-frame dcd file
This tool is helpful when one frame is needed but the entire trajectory is too large to transfer.
Convert NAMD binary restart file to amber restart ASCII restart file
Installing and compiling Amber12 with CUDA
of how to install and compile cuda toolkit and Amber12 for the GPU machine (ubuntu OS).
by Christopher C. Roberts and modified by Zhiye Tang
Organic Ligand Parameterization and Complexation with AMBER and AmberTools
Description of how to parameterize a custom organic ligand. Additionally describes how to form both a covalent and non-covalent complex with the newly parametrized ligand.
Written by Christopher C. Roberts
How to Run NAMD2 in Parrot of Biocluster using Charmrun
/opt/NAMD-2.7_Linux-x86_64-parrot/charmrun ++local ++p <procs> /opt/NAMD-2.7_Linux-x86_64-parrot/namd2 <configfile>