VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Nov 30 2015 - 23:51:22 CST

There are several options to save coordinate/structure files out of VMD.

 

Graphically:

VMD Main->Save Coordinates (Select molecule before in VMD Main with mouse)

 

Or from TCL console:

 

set molid 0

set desiredframe 0

animate write gro mynew.gro beg $desiredframe end desiredframe skip 1 $molid

 

Or from TCL console 2:

 

set molid 0

set desiredframe 0

set selection „all“

set a [atomselect $molid „$selection“ frame $desiredframe]

$a writegro mynew.gro

$a delete

 

Good luck

Norman Geist

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von James Lord
Gesendet: Montag, 30. November 2015 12:28
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: new structure file

 

Hi all,

I have a .gro file from Gromacs, I have modified the position of the protein in this .gro file after loading it into VMD and using

pbc wrap

now I want to save this .gro file with protein new position and use it as a start structure to continue my simulation? I could not figure out how to do this in VMD? any comments? I have periodic boundary condition in xyz.

Cheers,

James