VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Wed Feb 05 2014 - 14:20:17 CST

Dear Maxim,

I really appreciate. I have tried a lot to build such these trajectories
since two months ago, I hope I can do this by editing your code.

I really do not know what this error is. I just know, in my tk console
catdcd is not known but catdcdList is known.

On Wed, Feb 5, 2014 at 8:53 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> Ali,
>
> What is 'catdcdList'? From what I see, it gets called instead of catdcd.
> Run 'which catdcd' and post the result here.
> Here is a web-link to catdcd:
> https://www-s.ks.uiuc.edu/Development/MDTools/catdcd/
> Usually, when you call it with wrong arguments, you'll get more helpful
> information then what you got.
>
>
> Back to your code for "complex" trajectories. Your code is doing something
> weird - not what you describe. It'll be easier and faster if you start from
> scratch.
>
> Right now, I can think of a following way to achieve want you want for
> "complex" trajectories.
>
> 1. Load your "complex" trajectory:
>
>
> set xmol [mol load psf psf_file.psf]
> mol addfile trajectory.trr waitfor all $xmol
>
>
> 2. Create another molecule with X atoms (X - is the number of molecules
> whose centers of masses you want to track):
>
> set ntracked 100
>
> set ymol [mol new atoms $ntracked]; # change 100 to be the number of
> molecules
> set mov ""
> for {set i 0} {$i < $ntracked} {incr i} { lappend mov [atomselect $ymol
> "index $i"] }
> set all [atomselect $ymol all]
> $all set radius 1.0
> $all delete
> animate write psf com_traj.psf $ymol
>
>
> 3. Create list of selections of your real molecules, for example, for
> water molecules you could do something like:
>
>
> set water [atomselect $xmol "water"]
> set resids [lsort -unique [$water get resid]]
> $water delete
> set sel ""
> foreach resid $resids { lappend sel [atomselect $xmol "water and resid
> $resid"] }
>
>
> 4. Loop over trajectory frames, find center of masses of each real
> molecule and move atoms created in step 2 to computed locations:
>
>
> for {set i 0} {$i < [molinfo $xmol get numframes]} {incr i} {
>
> animate dup $ymol
>
> set atomindex 0
> foreach selection $sel {
>
> $selection frame $i
> set center [measure center $selection weight mass]
> [lindex $mov $atomindex] moveto $center
> incr atomindex
>
> }
>
> }
>
> animate write dcd com_traj.dcd $ymol
>
>
> 5. Delete all selection to clear-up memory
>
> foreach selection [atomselect list] { $selection delete }
>
>
>
> Maxim
>
>
> On Feb 5, 2014, at 5:31 AM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> wrote:
>
> 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
>
>
> 

-- 
Sincerely
Ali Alizadeh