VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 11 2013 - 23:53:59 CST

i already gave you my suggestion in a previous e-mail and that was
different from what you have implemented (which are not even half a
solution).

On Thu, Dec 12, 2013 at 12:29 AM, Ali Alizadeh
<ali.alizadehmoj_at_gmail.com> wrote:
>
> Dear Axel,
>
> I decided to start from a pdb file and then I find my trajectory file. I've
> written a simple tcl code for calculation of COMs of water molecules.
>
> My box includes 500 water molecules. I think it is correct I'm not sure. I
> want to save these coordinates in a new pdb file
>
> but I do not know how I can do this, Can you give me some advice?
>
> set file [open "COM.dat" w]
>
> for {set x 1} {$x <=500} {incr x} {
> puts $x
> set sel [atomselect top "resid $x"]
> puts $sel
> set selcom [measure center $sel]
> puts $selcom
> puts $file $selcom
>
>
> }
>
> close $file
>
>
>
>
> On Mon, Dec 9, 2013 at 10:43 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> wrote:
>>
>> 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
>
>
>
>
> --
> Sincerely
>
> Ali Alizadeh 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.