A great tool for coloring protein models based on RMSF per-residue obtained from molecular dynamics in Gromacs is available here. Nonetheless, I was unable to do the optimizations for NAMD-derived RMSF, but found another way to accomplish this. Using the Java-based Windows program named PDB Editor available here, I sort the atoms by atom name. All the CA atoms from all residues will be placed in ascending order (from the first to the last residue) and I simply overwrite the B column with the computed RMSF values. Then, I rearrange the PDB and save it, then load it in VMD where I color by B factor using custom color scales.
For further VMD and related scripts you may check the page of Ramin Ekhteiari Salmas, PhD, MRSC which features codes for calculating radius of gyration or number of water molecules in an active site.
I use BoxShade to create colorized multiple sequence alignments.
Daniel Șterbuleac 