VMD-L Mailing List
From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Mon Dec 09 2013 - 09:55:58 CST
Thank you very much for your reply.
I know I am ready for scripting but If possible I need some guides. I have
found I can calculate the COM of molecules but I do not know how I can
save them and write in to standard trajectory.
On Mon, Dec 9, 2013 at 6:32 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> Possible? Yes.
> Automatic? No.
> It would require quite a bit of custom vmd scripting. Not very difficult,
> but you would have to combine different pieces of scripting that have been
> discussed before.
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> *From: * Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> *Sender: * owner-vmd-l_at_ks.uiuc.edu
> *Date: *Mon, 9 Dec 2013 16:39:30 +0330
> *To: *Vmd l<vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: Atomic trajectory to COM trajectory,
> Dear All users,
> I have done an NVT ensemble with LAMMPS package. I have saved its
> trajectory in trr format.
> Now, I want to convert that atomic trajectory to trajectory of center of
> mass of molecules. Is it
> possible? Does any body have experience? I want to do this for calculation
> of density and g(r)
> values of COMs in VMD. Can I save the coordinates of atomic trajectory of
> atoms as COM
> Ali Alizadeh
-- Sincerely Ali Alizadeh