Pick one frame from namd dcd file and save it to another single-frame dcd file /home/sh_tzy/bin/DCDPick/, 138.23.56.82 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 /home/sh_tzy/bin/NAMD2PMEMD/, 138.23.56.82 Installing and compiling Amber12 with CUDA Description
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 AmberToolsDescription 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>
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