VMD-L Mailing List
From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 01 2015 - 01:26:52 CST
- Next message: Francesco Pietra: "Re: namd-l: Fwd: TIP4P and CHARMM27"
- Previous message: Norman Geist: "AW: new structure file"
- In reply to: Norman Geist: "AW: new structure file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Sry, it’s:
set molid 0
set desiredframe 0
animate write gro mynew.gro beg $desiredframe end $desiredframe skip 1 $molid
Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Norman Geist
Gesendet: Dienstag, 1. Dezember 2015 06:51
An: 'James Lord' <jjamesgreen110_at_gmail.com>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Betreff: AW: vmd-l: new structure file
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> [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von James Lord
Gesendet: Montag, 30. November 2015 12:28
An: <mailto:vmd-l_at_ks.uiuc.edu> 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
- Next message: Francesco Pietra: "Re: namd-l: Fwd: TIP4P and CHARMM27"
- Previous message: Norman Geist: "AW: new structure file"
- In reply to: Norman Geist: "AW: new structure file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]