VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Mon Dec 09 2013 - 10:26:49 CST

Dear Axel,

Thank you for your complete and useful reply. I'll try to write each
separately and then combine them.

On Mon, Dec 9, 2013 at 8:21 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Dec 9, 2013 at 4:55 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> wrote:
> > Dear Axel,
> >
> > 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.
>
> here is the recipe in 'vmd shorthand':
> you need to build a new molecule with "mol new atoms ###" where ### is
> the number of molecules, create a selection for this molecule
> containing all atoms with atomselect, and then loop over the existing
> trajectory, collect the COMs in a list of xyz coordinate triples,
> create a new frame in the new molecule with "animate dup", then step
> the selection to that frame and assign the coordinate list to the {x y
> z} property.
>
> once the loop is complete, you can save the new molecule as a .dcd or
> similar file. for easier processing, you may assign some other
> properties (type, name, mass, etc.) to the atoms in the molecule and
> write out a .psf file as well.
>
> more detailed explanations for all those steps are in the users guide
> and some examples for parts of these tasks are in some of the
> available tutorials as well. each step by itself is fairly simple, the
> complications come from having to combine and properly assemble all of
> them. you are better off first writing small test scriptlets where you
> practice each feature and piece separately until you are confident to
> know what you are doing. any more detailed guide would be the same as
> writing the script directly.
>
> axel.
>
> >
> >
> > 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.
> >>
> >> Axel.
> >> --
> >> 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
> >>
> >> trajectory?
> >>
> >>
> >> --
> >> Sincerely
> >>
> >> Ali Alizadeh
> >
> >
> >
> >
> > --
> > Sincerely
> >
> > Ali Alizadeh
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
Sincerely
Ali Alizadeh