VMD-L Mailing List

From: Chetan Mahajan (cmahajan_at_steinitz.che.utexas.edu)
Date: Tue Jun 09 2009 - 13:08:16 CDT

Thanks, Axel.
Sorry that it took some time before I could keep up with the issue.

I will take care not to cross-post in future, but for now, I am sending this
to both mailing lists, to share my information on lammps to vmd options.

So I tried with new 1.8.7 version.
Firstly, the issue of parser bug is solved, as you said.

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?

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.

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.

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??

Thanks very much
Regards
Chetan

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Axel Kohlmeyer
Sent: Thursday, May 28, 2009 10:32 AM
To: Chetan Mahajan
Cc: vmd-l_at_ks.uiuc.edu; lammps-users_at_lists.sourceforge.net
Subject: vmd-l: Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool

On Wed, 2009-05-27 at 17:39 -0500, Chetan Mahajan wrote:
> Hi

chetan,

please try not to cross post to mailing lists, but rather send
to individual lists, preferably the most relevant first. this
will make it easier on people to respond that are not subscribed
to both lists. thanks in advance.
 
> Well I am running into a very strange problem.

> Earlier I have successfully implemented lmp2vmd tool and generated
> sample snapshots...then I changed my system a little bit and to
> generate snapshots, I typed:
>
>
>
> mol new dump.micelle type lammpstrj waitfor all

now this looks like a pure VMD problem. this command is
not part of the lmp2vmd scripts.

> and it gave error as follows:
>

hmmm... it is difficult to quote and
reply to a gif image.

> And very strange, and surprising, that this builtup file which is
> exactly same as non-working file test14original.txt above, I working

correction, those two files are _not_ exactly the same.
the "original" has an additional blank after ITEM: ATOMS
and that makes all the difference.

[akohlmey_at_vitriol lammps-test]$ diff -u test14original.txt
test14builtup.txt
--- test14original.txt 2009-05-28 10:56:12.000000000 -0400
+++ test14builtup.txt 2009-05-28 10:56:05.000000000 -0400
@@ -6,7 +6,7 @@
 117.71 164.43
 117.71 164.43
 117.71 164.43
-ITEM: ATOMS
+ITEM: ATOMS
 1 6 161.807999 121.164001 119.483002
 2 4 161.727005 120.287003 119.950996
 3 1 160.871002 120.598000 120.980003

two files and you'll see there is a "transparent" difference.

> fine as follows:

> Could anybody give any clue as to what's happening here?

yes. this is due to a weakness of the parser in the lammps
molfile plugin in vmd-1.8.6. this has been resolved a few
weeks ago. i suggest you upgrade to the latest vmd-1.8.7
beta release, which contains these fixes and many additional
lammps related improvements, e.g. the option to read in
(and manipulate and write out) data files directly as new
molecules via the topotools package which will come with
VMD directly (as it is not limited to lammps).
the lmp2vmd scripts thus are becoming obsolete and i'd
like to encourage you to use topotools instead.

since the next version of VMD is going to be released
soon, i would particularly appreciate it, if you could
give it a try as soon as possible, so that potential
bugs (there is a lot of new code which is bound to have
bugs left in it) or missing features get discovered and
can (hopefully) be fixed or implemented before the release.

thanks,
   axel.

>
>
> Thanks in advance
>
> Chetan
>
>
>
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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