VMD-L Mailing List

From: Chetan Mahajan (cmahajan_at_steinitz.che.utexas.edu)
Date: Wed Jun 10 2009 - 10:00:30 CDT

Thanks, Axel.

 

1. I was searching topotools in users' guide or menu for 1.8.7

 

So if I figure out everything, I will give it a try sometime and pass one
the feedback..same for extending script for lmp2vmd tool..

 

2. Regarding my point 1 of resid tool, I just followed following
instructions in lmp2vmd README.

 

The script defines a new procedure "lmpresidfromdata". To activate it type

   at the VMD command prompt:

 

     source lmpresid2vmd.tcl

 

   To then add the residue information to a PSF file, see the steps for from

   item 1 from above and then type into the VMD console.

   

     lmpresidfromdata [molinfo top] data.micelle

 

Since I don't see any visible changes, I was wondering what it does, in
particular.

 

Another little thing is I find that the step "To then add the residue
information to a PSF file, see the steps for from

item 1 from above and" not needed, since we want to generate .psf file with
all the features of bonding, residue, atom names etc, if we repeat this " "
step everytime for all 4 steps in lmp2vmd README, then final .psf file is
not inclusive of all features. And since we want to load only one .psf file
with lammps trajectory, it's not desirable to repeat that step of loading
lammps traj every time. So I suggest removing those instructions from
README.

 

Thanks

Chetan

 

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_cmm.chem.upenn.edu]
Sent: Wednesday, June 10, 2009 8:37 AM
To: Chetan Mahajan
Cc: vmd-l
Subject: RE: vmd-l: Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool

 

On Tue, 2009-06-09 at 13:08 -0500, Chetan Mahajan wrote:

 

chetan,

 

please let me re-iterate. all your questions are pure VMD

questions and thus of little interest to the vast majority

of LAMMPS users. i'm thus removing the cc to the lammps list.

 

> So I tried with new 1.8.7 version.

> Firstly, the issue of parser bug is solved, as you said.

 

thanks. that is good to know.

 

> Secondly, I searched for topotools package so that I can test it, but no

> where did I find its tutorial or option in the menu. Could you direct me
to

> it, please?

 

i don't know how you are searching for something, but i just

typed "topotools" into google and the third hit was the topotools

plugin documentation on the VMD homepage.

http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

 

topotools is a pure script extension without a gui

(so is lmp2vmd), so it cannot show up in the extensions

menu. BTWL i had just recently before your question posted

an announcement about this package and the VMD beta

to the LAMMPS mailing list.

 

> Thirdly, now lmp2vmd script works, but I have little issues there:

>

> 1. I don't see any visible changes happening after I implement residue
tool,

> in option b.

 

i am sorry, but you have to describe in detail what you did

and then i can comment on what went wrong or what is supposed

to happen. this statement tells me nothing an i don't want to

guess what you were doing.

 

as i stated before, my advice is to use the topotools package,

particularly using topo readlammpsdata should allow you to

read the lammps data file directly _including_ bonds in one go.

 

> 2. I can use coloring by atom name so that it gives different colors to

> different atoms. This is desirable for polymer molecule, but not for
polymer

> and solvent molecules together if they have same atoms. So in addition, I

> want to assign different colors to different molecules, even though they

> carry same atoms, how to do that? that means I want to use atom name

> coloring selectively for polymer chain, but for different solvent
molecules

> like water and methanol, I want to use different colors, even though same

> atoms are also there in polymer chain. IN my data file, I have different

> atom types for "such same" atoms, but belonging to different molecules,
but

> I don't see that vmd is taking that information in, even though in
lmptoname

> tool I use "H1 H2 H3 etc". I guess it assigns same color to same atom

> belonging to different molecules.

 

please don't guess, but read the VMD documentation. VMD is by design a

very simple minded program, it displays what you feed it in a simple

way. it cannot read your mind and figure out what you intend to show.

as for coloring by name, you have to keep in mind that VMD disregards

the number part of the atom name, as per convention for biomolecules.

however, you can use the color script command to adjust your colormap

or the color dialog in the VMD GUI.

 

> So with my limited knowledge, this can be solved by, (a)either assigning

> different colors to different atom "types as defined in my data file" (b)

> different colors to different molecules, in addition to atom color

> differentiation in polymer chain.

>

> How to do that??

 

write additional scripts. this is exactly _why_ VMD has an

embedded script interpreter. nobody can foresee all the potential

uses of VMD, and thus it is much simpler to augment the existing

features with a little scripting rather than trying to implement

it all into the GUI (well, even GUIs can be scripted).

 

cheers,

    axel.

 

>

> Thanks very much

> Regards

> Chetan

>

 

  

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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