VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Nov 17 2016 - 02:05:46 CST

Hey,

 

thanks for your work so far. Would it be difficult to also implement a unwrap function (more or less remove long bonds)? Since f.i. GROMACS outputs trajectories always wrapped.

 

Norman

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Jérôme Hénin
Gesendet: Mittwoch, 16. November 2016 14:55
An: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Betreff: vmd-l: Fast PBC wrapping in VMD

 

Hi everyone,

 

This is a reminder that there is a faster alternative to pbc wrap from the PBCTools plugin, in the form of qwrap:

https://github.com/jhenin/qwrap

 

It has improved since the last time I mentioned it on this list, specifically, you can now restrict the wrapping to a given selection, as in (my personal favorite):

qwrap sel "not protein" center protein

 

Thanks to a contribution by Giacomo Fiorin, wrapping can also be done based on VMD fragments.

 

Qwrap is written in C and is relatively simple-minded, hence the speed. The main limitation with respect to pbc wrap is the treatment of orthorhombic cells only - however that can change in the future.

 

As usual, feedback is welcome.

 

Jerome