From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Wed Feb 05 2014 - 05:31:39 CST

Dear Maxim,

I've got below error when I wanted to write new trr as you said.

catdcd -otype trr -o output.trr -i index.txt traj_nvt.lammpstrj:

wrong # args: should be "catdcdList dcdFileNames outFile indexFile stride"

-----------

On Wed, Feb 5, 2014 at 1:30 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> Hi Ali,
>
> If you want to save centers of mass of water molecules only, you should
> use the fact that its COM is very close to its oxygen atom. Then, you can
> simply extract trajectories of all water oxygens from your TRR file. To do
> that:
>
> 1. Load your psf/pdb or just pdb file into VMD
>
> 2. Make a selection of necessary oxygens, like:
>
> set sel [atomselect top "name OH2"]; # or set sel [atomselect top "oxygen"]
>
>
> 3. Write their indices:
>
> set ch [open "oxygen_indices.txt" w]
> puts $ch [$sel get index]
> close ch
>
>
> 4. Use catdcd to extract trajectory for those oxygen atoms
>
> catdcd -otype TRR -o output.trr -i oxygen_indices.txt your_input_file.trr
>
>
> Try that and let us know if it works for you.
>
> Maxim
>
>
>
> On Feb 4, 2014, at 3:21 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> wrote:
>
> 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
>
>
>

-- 
Sincerely
Ali Alizadeh