VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Tue Feb 04 2014 - 15:21:03 CST

Dear Axel,

I asked you a question about saving COM trajectory fro atomic trajectories.
I've written this code but I can not save the coordination of each atom as
a standard COM

trajectory. This code can calculate the COM of each atom in each frame. I
need your advice for building COM trajectory. My simulation box includes
500 water

molecules.

-------------

set file [open "COM.xyz" w]
set nf [molinfo top get numframes]
for {set i 0} {$i <=$nf} {incr i} {animate dup frame $i
   animate goto $i} {
                puts $file "500"
                puts $file "frame $i"
                puts "frame $i"
                for {set x 0} {$x <=1500} {incr x 3} {
                    set sel [atomselect top "index $x" frame $i]
                    set com [measure center $sel weight [$sel get mass]]
                    puts $file "C $com"
                }

}

close $file

---------------------

On Mon, Dec 9, 2013 at 7:56 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>wrote:

>
> 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
> 

-- 
Sincerely
Ali Alizadeh