Jekyll2024-01-11T23:05:15+00:00https://zyumse.github.io/feed.xmlNotes along with my research, particularly on computational methods, molecular dynamics, machine learning, etc.2024-01-06T00:00:00+00:002024-01-06T00:00:00+00:00https://zyumse.github.io/ABC<ul> <li>generate a tinker format xyz file <ul> <li>~/projects/bin-macos/pdbxyz file.pdb</li> </ul> </li> <li>change the numeric types in the xyz file (to those in PRM )</li> <li>~/projects/bin-macos/minimize P4_CH3.xyz, with the PRM file –&gt; .xyz_2</li> <li>use charges from ORCA to update the PRM file</li> <li>redo minimize –&gt; .xyz_3</li> <li>~/projects/bin-macos/analyze P4_CH3.xyz_2 Moreno.prm P &gt; out</li> <li>remove the useless header ### in out</li> <li>python tinkertoLAMMPS.py</li> </ul>

generate a tinker format xyz file ~/projects/bin-macos/pdbxyz file.pdb change the numeric types in the xyz file (to those in PRM ) ~/projects/bin-macos/minimize P4_CH3.xyz, with the PRM file –&gt; .xyz_2 use charges from ORCA to update the PRM file redo minimize –&gt; .xyz_3 ~/projects/bin-macos/analyze P4_CH3.xyz_2 Moreno.prm P &gt; out remove the useless header ### in out python tinkertoLAMMPS.py