cpptraj
cpptraj copied to clipboard
Amber-MD
Biomolecular simulation trajectory/data analysis.
Some ideas, as discussed in FL: -Membrane curvature -Area per lipid (taking into account proteins/objects embedded) -Local membrane thickness/surface perturbation
Problem is related to `origincut` and `zcut` (stagger), which have different values for non-canonical pairs.
Currently goes by lipid chain only.
If mask1 is residues 1 to 10 and mask2 is residues 11 to 15, want a 10x5 matrix, not 15x15 (lots of wasted space).
Something like: ``` rotate usedata Rmatrix aroundz ``` for only rotations around Z.
Do not require output file [out <filename>] / reduce Action/Analysis verbosity for libcpptraj/pytraj
I am not sure if we chat about this. What's you opinion about strictly requiring output filename? If the Action is used in pytraj, I prefer to have the filename...
Hi, This command will dump output to CpptrajState `spam peaks.xyz name SPAM cut 12.0 info spam.info out spam.dat reorder summary summary.dat` This does not: `spam peaks.xyz cut 12.0 reorder`
Currently during `diagmatrix` eigenvalues calculated from a mass-weighted covariance matrix are always converted to frequencies. There should be an option not to do this, and if it happens things like...
If time is present in trajectory files, use it when setting up data sets.
Give the user an indication that something is still happening.