From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Sep 26 2013 - 00:45:38 CDT
You need to type it to the representations to check your selection,
afterwards File->save coordinates with the same selection text.
Norman Geist.
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Mittwoch, 25. September 2013 21:08
An: Norman Geist
Betreff: Re: namd-l: Coordinates of Carbon atoms on Graphite
I get:
vmd > [atomselect top all] move [transaxis z 45]
vmd > y>-1.4
invalid command name "y>-1.4"
On Wed, Sep 25, 2013 at 10:16 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Simply generated by :
1. [atomselect top all] move [transaxis z 45]
2. Selecting the two rows by "y > -1.4"
3. Save coordinates by using "y > -1.4"
4. Load the new pdb into new mol
5. [atomselect top all] move [transaxis z -45]
6. Save coordinates again
That's it.
Norman Geist.
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Mittwoch, 25. September 2013 15:41
An: Norman Geist
Betreff: Re: namd-l: Coordinates of Carbon atoms on Graphite
Here is pdb file.
Thank you,
Mihaela
On Wed, Sep 25, 2013 at 9:35 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
I have no idea how you layers look like, but for example by using coordinate
atom selections like "y > 0". By labeling one atom (pressing "1") u can get
a reference coordinate for the dimension you need in your case. Afterwards
use "save coordinates" with the selection worked. Otherwise, show me you
pdb.
Norman Geist.
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Mittwoch, 25. September 2013 13:56
An: Norman Geist
Betreff: Re: namd-l: Coordinates of Carbon atoms on Graphite
Hi,
So far, all pdb files for graphite show four layers.I only need two layers,
not four. How can I get VMD to show two layers only?
Mihaela
On Wed, Sep 25, 2013 at 1:49 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Why not, but why heteronymous?
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Mihaela Drenscko
Gesendet: Dienstag, 24. September 2013 18:47
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Coordinates of Carbon atoms on Graphite
Hello,
I have to run a namd simulation for the interaction between a nano-sized
water droplet and graphite substrate. Can I use VMD to display the
coordinates of atoms in two heteronymous layers of hexagonal graphite?
Thank you,
Mihaela
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