cpptraj

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Puzzled by atom-based masking of energies

1

I want to decompose the energies of a system by atom, but am puzzled by the outputs. I'm using commands of the form energy test1 @2 out test1.txt energy test2...

mkgilson

Right now `multidihedral` requires all 4 atoms be bonded. Should there be a keyword (or on by default) that all atoms do not need to be bonded?

drroe

modXNA is a method for generating non-standard amino acid residues. It would be nice if `prepareforleap` could interface with this in some way. https://modxna.chpc.utah.edu/

drroe

Regarding the Principal component analysis with CPPTRAJ

4

Hi Users/Developers, I am having issues running PCA analysis with CPPTRAJ. It always stops showing the segmentation fault. I am only considering the CA atoms of protein and P atoms...

satyajitkhatua09

Conda package for cpptraj

14

@drroe This is actually my first attempt at a pull request that is based on a non-master branch. I'm assuming that accepting the request will create a `conda` branch at...

dacase

Create a conda package

18

This would make it easier for cpptraj to be part of Amber Classic

drroe

Shift in grid-based calculations

6

Hi all, I am running GIST on some small molecules and the resulting maps for all the calculated quantities are shifted in space relative to the solute. I am getting...

choutkaj

Allow atommap rmsfit to proceed with partial atom maps

4

6.29.8. Previously `atommap rmsfit` required a full atom mapping to work. This PR changes it so that only the mapped atoms are used in the rms fit. It also adds...

drroe

How best to handle cpptraj vs. cpptraj.{MPI,OMP,cuda}

5

The Amber24 Reference Manual describes MPI and OMP parallelization, but is not very clear about which executables do what. For example, if I configure (using the Makefile) with the -openmp...

dacase

The current release is more than 2 years ago and we have a lot of useful updates. Like running GIST in parallel. I think it would be good to do...

xiki-tempula