cpptraj
cpptraj copied to clipboard
Amber-MD
Biomolecular simulation trajectory/data analysis.
I want to calculate DNA elasticity using CPPTRAJ. This is compatible in gromacs https://do-x3dna.readthedocs.io/en/latest/about_dna_elasticity.html Is It possible to calculate DNA elasticity using CPPTRAJ
A lot of the framework is already there from the `rst` command. Will likely be easier to maintain, and will make it easy to add functionality like mask selection (to...
related to https://github.com/Amber-MD/cpptraj/issues/175, https://github.com/Amber-MD/cpptraj/issues/93 I will keep updating checklist in 1st post and post the detail in following post. - [ ] Action_NativeContact - [ ] Select dihedral, angle (bond...
Currently you need to specify some sort of data set to cluster on, but it's not strictly necessary. Issue was raised by user Tim Davis on the Amber mailing list....
Now in Ang/(1/20.455) ps - users may want it converted.
Also, the fact that distances are not imaged by default should be stated in the manual.
Right now must be loaded with the `reference` command, which is not convenient.
Hi, Hi, I was trying to find out whether we could use SPAM (equations) for calculating interaction energies for small solvent molecules apart from Water, for example if i have...
hi, writing `.xyz` format is ok in pytraj but getting error for reading. ``` In [12]: traj = pt.load('../tz2.crd', '../tz2.parm7') In [13]: traj.save("test.xyz") In [14]: pt._verbose() In [15]: pt.load("test.xyz", traj.top)...