[CPMD-list] from younes ansari

[Axel Kohlmeyer]

On Mon, 7 Feb 2005, Younes Ansari wrote:

YA> Dear CPMD users

dear younes ansari,

first off a few remarks.

- please use a subject line that has some relevance
  to the question you ask. this makes it easier to
  follow a thread. we already know from the From:
  line, that you have sent the mail.

- there is no need to send your mail twice, and
  also using HTML encoding is at best redundant 
  and annoying to others. please see: http://expita.com/nomime.html
  
- in a previous mail i have already pointed you to:
  http://www.catb.org/~esr/faqs/smart-questions.html
  please read it again and follow the advice, if you
  want to get useful answers. it is extremely difficult
  to guess the (vital) parts, that you are leaving out,
  so chances are, that people will ignore you, or 
  - even worse - give bad advice.


YA> I have a very simple question: once a CPMD run is through, the
YA> trajectories in VMD environment look to have extra line as if some 
YA> atoms are bonded by more than their bonds by more than their valance bond. 
YA> For example, an H atom is bonded to other three C atoms. This is the case 
YA> for other elements.

please give more details here and post a (short) example.
if i assume that you are loading a GEOMETRY.xyz
or TRAJEC.xyz file generated by CPMD into the VMD visualization
program (note, that people here may know CPMD, but not 
necessarily VMD), then wrong bonding like you describe it,
most likely originates from providing coordinates in angstrom 
while not using the ANGSTROM keyword. please note, that 
VMD does not recompute the bonding when visualizing a trajectory
unless you use the Dynamic Bonds representation (or something
more sophisticated). you can find an example at:
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part2.html#chap4_sect5

YA> The input file representing the molecule is originally made in
YA> HYPERCHEM, and then operated for appropriate coordinate in GAUSSIAN 98
YA> where it allows the input file for CPMD be formatted suitably.

i am sorry, but i cannot follow you here. how should a run
with gaussian help you to get correctly formatted CPMD input?
can you please explain the procedure in more detail.

YA> 
YA> It might be due by the representation and not really extra bonds are
YA> involved. Could any of you give comment on this!

as far as VMD visualization is concerned, the VMD mailing
list may be a better place to discuss that. but please first
make sure, that your CPMD input is correct.
a finished CPMD run without any error messages is a 
prerequisite for that but not a sufficient indicator.

best regards,
	axel kohlmeyer.

YA> 
YA> 
YA> 		
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-- 

=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.