VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Mon Dec 09 2013 - 13:13:49 CST

Dear Axel,

Okay,

On Mon, Dec 9, 2013 at 11:09 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> You have to do what your data requires.
> --
> 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>
> *Date: *Mon, 9 Dec 2013 10:43:57 -0800
> *To: *Axel Kohlmeyer<akohlmey_at_gmail.com>
> *Cc: *Vmd l<vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: Atomic trajectory to COM trajectory,
>
> Dear Axel,
>
> I have a question, Is it necessary to use wrap command for wrapping my
> trajectory before I start scripting?
>
>
> On Mon, Dec 9, 2013 at 8:26 AM, 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