I received some clarification off-list and looked into what was going on. The system is a solvated protein. The initial pdb and crd files were generated by tleap. cpptraj was then used to read the crd file, recenter the protein, and wrap the waters to produce a new crd file. vmd was then used to visualize the pdb file and the manipulated (centered/wrapped) crd files. By default, vmd only shows the primary unit cell. The visualization of the (unmanipulated) pdb file's primary unit cell didn't show any "gaps" in the solvent, whereas the manipulated crd file does show gaps. However, if one tells vmd to display the primary and neighboring cells, one can see gaps between the cells in both files because the system hasn't yet been equilibrated at constant pressure. The only reason why the manipulated crd file shows gaps in the primary unit cell was because cpptraj was used to translate the coordinates.
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Received on Thu Aug 07 2025 - 09:00:02 PDT
