VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Oct 27 2015 - 06:28:09 CDT

Do I understand correctly that you want to measure the thickness of the hydration shell of a protein from a simulation output?

 

Norman Geist

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von sunyeping
Gesendet: Dienstag, 27. Oktober 2015 06:51
An: vmd-l <vmd-l_at_ks.uiuc.edu>
Betreff: vmd-l: how to measure the thickness of the water shell

 

 

Dear all,

 

By vmd we can add water shell box around a protein by command like: solvate protein.psd protein.pdb -t 10. The option -t is the thickness of the water shell to be added.

But as for a exited water box, how to measure the thickness of the water shell?

 

Best regards.

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences