[SIESTA-L] LDAU version

[Bin Shao]

Dear all,

I intend to do a calculation with LDAU method, so I download the siesta ldau
version and complie it successfully. I test it with the examples in source
package and everything goes well. But when I start with my ZnO input file,
the program stuck and the following is the output file. I have check the
calcultion with the command $top, the result shows the calculation is still
working.


..
siesta: k-grid: Number of k-points =   683
siesta: k-grid: Cutoff (effective) =20.822 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:   13   0   0  0.000
siesta: k-grid:0  13   0  0.000
siesta: k-grid:0   0   8  0.000
Naive supercell factors: 775
superc: Internal auxiliary supercell: 7 x 7 x 5  = 245
superc: Number of atoms, orbitals, and projectors:980 13720 15680
 stuck at here

But when I use the normal version of siesta with the same input file, the
calculation will go on. What is the problem? And the attachment is my input
file, please give me some suggestions.

Best regards,

Bin Shao


-- 
Bin Shao, Ph.D. Candidate
College of Information Technical Science, Nankai University
94 Weijin Rd. Nankai Dist. Tianjin 300071, China
Email: binshao1...@gmail.com


input.fdf
Description: Binary data

Re: [SIESTA-L] Off-topic: Vesta

[Ricardo Faccio]

Hi Eric
The process is as following:
Edit-> Structure-> Remove Symmetry -> Apply!
Remember to save a cif file!
Regards
Ricardo
> Hey Ricardo,
>
> May I ask you how do you save a structure with the P1 symmetry.
> Actually, when I set the symmetry to P1 and save it, it does not seem to
> work.
> Yours,
>
>   Eric.
>
> On 04/06/2011 09:52 AM, Ricardo Faccio wrote:
>> Hi Marcos
>> I think that you procedure is fine. The problem with vesta is that it
>> needs yo save changes by step. I mean, first Open your file and remove
>> the symmetry, and get a p1 structure. Then save it as a cif file.
>> Afyer this read this file and perform the transformation, and save it
>> as a different cif file. Finally load it and apply the symmetry, if
>> you want, and get another cif file. If you have further problems send
>> me your sf and i'll try to check it
>> Regards
>> Ricardo
>>
>> 
>> Dr. Ricardo Faccio
>> Prof. Adj. de Física
>>
>> Av. Gral. Flores 2124. CC 1157. CP 11800.
>> Phone: + 598 2 924 9859
>> Fax: + 598 2 924 1906
>> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
>> -
>>
>> El 06/04/2011, a las 10:27, Marcos Veríssimo Alves
>>  escribió:
>>
>>> Hi all,
>>>
>>> So, great to know there are knowledgeable people on Vesta in the
>>> mailing list. My question is the following: I have a cubic structure,
>>> a perovskite. I have a [sqrt(2) x sqrt(2)] cell of this structure,
>>> with relaxed positions with rotated oxygen octahedra in the x-y plane
>>> only, out of which I would like to create a [2 x 2] cell. I actually
>>> managed to do it (using a xsf file that i created from the xyz
>>> output), but in a way which I would not call the most elegant. It is
>>> also a way that is more prone to errors, than I wish it were.
>>>
>>> The problem is, when one loads an xsf file with the coordinates in
>>> Vesta, it displays a structure with more atoms than the unit cell
>>> actually does, and apparently it is the equivalent of XCrysDen's
>>> conventional cell mode. However, one can choose, in XCrysDen, to
>>> display only the translational asymmetric unit. This is one thing I
>>> don't know how to do in Vesta. For a matter of convenience (laziness,
>>> actually :) ), I have set both PRIMVEC and CONVVEC to the cubic
>>> lattice vectors, in the xsf file.
>>>
>>> Although I have managed to create a [2 x 2] cell, starting from the
>>> [sqrt(2) x sqrt(2)] using a transformation matrix (easy to deduce), I
>>> have to eliminate some atoms by setting boundaries to the fractional
>>> coordinates and checking that the number of atoms is actually the
>>> expected number. In the case of a [2 x 2] cell, of course, we have 4
>>> times as many atoms as in the [1 x 1] cell. However, I would be more
>>> reassured if there were an automatic way to guarantee that the
>>> correct number of atoms would be output, instead of having to make
>>> somewhat extensive checks to ensure this.
>>>
>>> Another doubt is about symmetrization of atomic coordinates. If I
>>> choose a space group for Vesta to symmetrize the atoms' coordinates,
>>> it ends up creating extra atoms which I can't seem to eliminate - at
>>> least i don't know the correct way to do it. I have tried the option
>>> "remove duplicate atoms", but it didn't work. Has anyone run into
>>> such problems?
>>>
>>> If things are not clear, I'll be glad to provide an xsf file to
>>> illustrate the issues.
>>>
>>> Best regards,
>>>
>>> Marcos
>>
>
> --
> /Be the change you wish to see in the world
> / — Mahatma Gandhi —
>
> Dr. Éric Germaneau 
>
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
>
> /Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /
>
>


-- 
-
  Dr. Ricardo Faccio
  Prof. Adjunto de Física
  Mail: Cryssmat-Lab., Cátedra de Física, DETEMA
  Facultad de Química, Universidad de la República
   Av. Gral. Flores 2124, C.C. 1157
   C.P. 11800, Montevideo, Uruguay.
  E-mail: rfac...@fq.edu.uy
  Phone: 598 2 924 98 59
 598 2 929 06 48
  Fax:   598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm

Re: [SIESTA-L] 5th Nano & Giga Forum in Russia

[uma shankar sharma]

I am interested. what about the registration fee & travelling grant


On 3/30/11, Anatoli Korkin  wrote:
> Nano & Giga Challenges in Electronics, Photonics & Renewable Energy
> (NGC2011)
> Symposium and Summer School (Tutorial Lectures)
> Moscow-Zelenograd, Russia, September 12-16, 2011
>
>
> The conference organizers invite academic, industry and government
> researchers, students, engineers,
> entrepreneurs and business leaders to participate in NGC2011 Symposium and
> Summer School. The conference
> will take place from September 12 to 16, 2011 at Moscow State University and
> in Zelenograd, suburban city
> of Moscow, where several leading Russian education and research centers and
> production facilities related
> to the electronics are located.
>
> On-line registration is available at the conference web site:
>
> http://www.asdn.net/ngc2011/
>
> The conference topics include nanoelectronics, photonics, and renewable
> energy research and technology
> development. Our meeting includes Summer School (tutorial lectures),
> symposium and satellite workshops
> on nanotechnology instrumentation and nano metrology and standardization.
> All sessions are coherently
> linked to each other and to social events designated to create an exciting
> 'mixer' with unique networking
> environment.
>
> This international interdisciplinary meeting offers unique opportunities for
> exchange of expertise,
> learning and networking by bringing together renowned researchers, young
> talents, creative engineers,
> entrepreneurs and business leaders. The focal points of our meeting include
> emerging materials and novel
> devices, Science and technology challenges and solutions for information
> technology (electronics and
> photonics), and alternative (solar and bio) energy. While covering broad
> areas of research and technology
> development, from semiconductors to biomolecules, the meeting is bridging
> fundamental scientific research
> and development of advanced products and disruptive technologies.
>
> For further information, registration and abstract submission, please, visit
> our web site:
>
> http://www.asdn.net/ngc2011
>
> We look forward to seeing you at 5th Nano & Giga Forum in Russia.
>
> NGC2011 Organizers
>
>
>
>
>

Re: [SIESTA-L] Strange Mulliken Charges

[Nicolas Leconte]

Hello,

I don't know for your specific system.

Mulliken is known to not be very reliable under many circumstances, even for
very small systems. Browse the archive of the mailing list, you'll find
several examples of this. The main problem is that a Mulliken charge
integration is basis dependent... depending on how you build your basis, you
can get very different and sometimes plain wrong results.

As you say, there exist several alternatives that do not share this weak
spot. You've may have heart of Bader, Voronoi or Hirschfeld analyses. They
are not yet included in the official release of Siesta, so you'll have to
hope some user is willing to share his implementation or do it yourself.

Other less important factors can also influence your results. I remember *J.
Phys. Chem. A **2002, **106, *12376-12385 discussed this for Si-O systems,
by comparing Mulliken, Hirshfeld and Bader. I haven't read it for quite a
while, but it should be easily transposable to your system.

Sincerely,
Nicolas

On Wed, Apr 6, 2011 at 4:00 PM, Michael Schuch  wrote:

>
> Dear Colleagues,
> I trying to estimate (at least on a qualitative level), where the
> electrons are located in the environment of 3- and 4-fold oxygen
> coordinated boron atoms. But i found a strange result for the Mulliken
> charges, since the electro-negativity of boron (approx 2.0) is much lower
> than the  electro-negativity of oxygen (approx. 3.5) i would expect
> naivly, that the charges are more located near the oxygen but i get
> following result* for the mulliken charges
> O approx. 5.9 and B approx. 3.2, i.e. the boron is negative charged and
> the oxygen is slightly positive charged. Hence I have some questions (i)
> How good is the (possible) correlation between Difference of the
> (macroscopic) electro-negativity and the Mullikencharges?
> (ii) Are the mulliken charges the right meassure for information about
> local charges (in the strict classical sense, i.e. a charge which acts as
> a effective source of coulomb interactions).
> (iii) If not- There is a big number of different definitions of effective
> charges beside the Mullikencharges. Whats the best choice of effective
> charges in the view of a optimal compromise between computational effort
> (i.e. lowest possible expense of programming time to extract the
> informations from siesta output) and physical meaning (I want to use this
> to estimate an effective coulomb interaction)?
>
> I thank you in advance
> Michael
>
> * Investigating by small clusters (20-30 aotm) using PBE and a
> PAO.Energyshift of 0.001
>
>
>
>
> --
> Michael Schuch
> FB. Physik / AG. Statistische Physik
> Barbarastrasse 7
> 49069 Osnabrück
>

Re: [SIESTA-L] Off-topic: Vesta

[Eric Germaneau]

Hey Ricardo,

May I ask you how do you save a structure with the P1 symmetry.
Actually, when I set the symmetry to P1 and save it, it does not seem to 
work.

Yours,

 Eric.

On 04/06/2011 09:52 AM, Ricardo Faccio wrote:

Hi Marcos
I think that you procedure is fine. The problem with vesta is that it 
needs yo save changes by step. I mean, first Open your file and remove 
the symmetry, and get a p1 structure. Then save it as a cif file. 
Afyer this read this file and perform the transformation, and save it 
as a different cif file. Finally load it and apply the symmetry, if 
you want, and get another cif file. If you have further problems send 
me your sf and i'll try to check it

Regards
Ricardo


Dr. Ricardo Faccio
Prof. Adj. de Física

Av. Gral. Flores 2124. CC 1157. CP 11800.
Phone: + 598 2 924 9859
Fax: + 598 2 924 1906
Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
-

El 06/04/2011, a las 10:27, Marcos Veríssimo Alves 
 escribió:



Hi all,

So, great to know there are knowledgeable people on Vesta in the 
mailing list. My question is the following: I have a cubic structure, 
a perovskite. I have a [sqrt(2) x sqrt(2)] cell of this structure, 
with relaxed positions with rotated oxygen octahedra in the x-y plane 
only, out of which I would like to create a [2 x 2] cell. I actually 
managed to do it (using a xsf file that i created from the xyz 
output), but in a way which I would not call the most elegant. It is 
also a way that is more prone to errors, than I wish it were.


The problem is, when one loads an xsf file with the coordinates in 
Vesta, it displays a structure with more atoms than the unit cell 
actually does, and apparently it is the equivalent of XCrysDen's 
conventional cell mode. However, one can choose, in XCrysDen, to 
display only the translational asymmetric unit. This is one thing I 
don't know how to do in Vesta. For a matter of convenience (laziness, 
actually :) ), I have set both PRIMVEC and CONVVEC to the cubic 
lattice vectors, in the xsf file.


Although I have managed to create a [2 x 2] cell, starting from the 
[sqrt(2) x sqrt(2)] using a transformation matrix (easy to deduce), I 
have to eliminate some atoms by setting boundaries to the fractional 
coordinates and checking that the number of atoms is actually the 
expected number. In the case of a [2 x 2] cell, of course, we have 4 
times as many atoms as in the [1 x 1] cell. However, I would be more 
reassured if there were an automatic way to guarantee that the 
correct number of atoms would be output, instead of having to make 
somewhat extensive checks to ensure this.


Another doubt is about symmetrization of atomic coordinates. If I 
choose a space group for Vesta to symmetrize the atoms' coordinates, 
it ends up creating extra atoms which I can't seem to eliminate - at 
least i don't know the correct way to do it. I have tried the option 
"remove duplicate atoms", but it didn't work. Has anyone run into 
such problems?


If things are not clear, I'll be glad to provide an xsf file to 
illustrate the issues.


Best regards,

Marcos




--
/Be the change you wish to see in the world
/ — Mahatma Gandhi —

Dr. Éric Germaneau 

College of Physical Sciences
Graduate University of Chinese Academy of Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html /

Re: [SIESTA-L] Off-topic: Vesta

[Marcos Veríssimo Alves]

Thanks Ricardo! I'll try to do that and I'll let you know the outcome.

Cheers,

Marcos

On Wed, Apr 6, 2011 at 3:52 PM, Ricardo Faccio  wrote:

> Hi Marcos
> I think that you procedure is fine. The problem with vesta is that it needs
> yo save changes by step. I mean, first Open your file and remove the
> symmetry, and get a p1 structure. Then save it as a cif file. Afyer this
> read this file and perform the transformation, and save it as a different
> cif file. Finally load it and apply the symmetry, if you want, and get
> another cif file. If you have further problems send me your sf and i'll try
> to check it
>
> Regards
> Ricardo
>
> 
> Dr. Ricardo Faccio
> Prof. Adj. de Física
>
> Av. Gral. Flores 2124. CC 1157. CP 11800.
> Phone: + 598 2 924 9859
> Fax: + 598 2 924 1906
> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
> -
>
> El 06/04/2011, a las 10:27, Marcos Veríssimo Alves <
> marcos.verissimo.al...@gmail.com> escribió:
>
>
>  Hi all,
>>
>> So, great to know there are knowledgeable people on Vesta in the mailing
>> list. My question is the following: I have a cubic structure, a perovskite.
>> I have a [sqrt(2) x sqrt(2)] cell of this structure, with relaxed positions
>> with rotated oxygen octahedra in the x-y plane only, out of which I would
>> like to create a [2 x 2] cell. I actually managed to do it (using a xsf file
>> that i created from the xyz output), but in a way which I would not call the
>> most elegant. It is also a way that is more prone to errors, than I wish it
>> were.
>>
>> The problem is, when one loads an xsf file with the coordinates in Vesta,
>> it displays a structure with more atoms than the unit cell actually does,
>> and apparently it is the equivalent of XCrysDen's conventional cell mode.
>> However, one can choose, in XCrysDen, to display only the translational
>> asymmetric unit. This is one thing I don't know how to do in Vesta. For a
>> matter of convenience (laziness, actually :) ), I have set both PRIMVEC and
>> CONVVEC to the cubic lattice vectors, in the xsf file.
>>
>> Although I have managed to create a [2 x 2] cell, starting from the
>> [sqrt(2) x sqrt(2)] using a transformation matrix (easy to deduce), I have
>> to eliminate some atoms by setting boundaries to the fractional coordinates
>> and checking that the number of atoms is actually the expected number. In
>> the case of a [2 x 2] cell, of course, we have 4 times as many atoms as in
>> the [1 x 1] cell. However, I would be more reassured if there were an
>> automatic way to guarantee that the correct number of atoms would be output,
>> instead of having to make somewhat extensive checks to ensure this.
>>
>> Another doubt is about symmetrization of atomic coordinates. If I choose a
>> space group for Vesta to symmetrize the atoms' coordinates, it ends up
>> creating extra atoms which I can't seem to eliminate - at least i don't know
>> the correct way to do it. I have tried the option "remove duplicate atoms",
>> but it didn't work. Has anyone run into such problems?
>>
>> If things are not clear, I'll be glad to provide an xsf file to illustrate
>> the issues.
>>
>> Best regards,
>>
>> Marcos
>>
>

[SIESTA-L] Strange Mulliken Charges

[Michael Schuch]

Dear Colleagues,
I trying to estimate (at least on a qualitative level), where the
electrons are located in the environment of 3- and 4-fold oxygen
coordinated boron atoms. But i found a strange result for the Mulliken
charges, since the electro-negativity of boron (approx 2.0) is much lower
than the  electro-negativity of oxygen (approx. 3.5) i would expect
naivly, that the charges are more located near the oxygen but i get
following result* for the mulliken charges
O approx. 5.9 and B approx. 3.2, i.e. the boron is negative charged and
the oxygen is slightly positive charged. Hence I have some questions (i)
How good is the (possible) correlation between Difference of the
(macroscopic) electro-negativity and the Mullikencharges?
(ii) Are the mulliken charges the right meassure for information about
local charges (in the strict classical sense, i.e. a charge which acts as
a effective source of coulomb interactions).
(iii) If not- There is a big number of different definitions of effective
charges beside the Mullikencharges. Whats the best choice of effective
charges in the view of a optimal compromise between computational effort
(i.e. lowest possible expense of programming time to extract the
informations from siesta output) and physical meaning (I want to use this
to estimate an effective coulomb interaction)?

I thank you in advance
Michael

* Investigating by small clusters (20-30 aotm) using PBE and a
PAO.Energyshift of 0.001




-- 
Michael Schuch
FB. Physik / AG. Statistische Physik
Barbarastrasse 7
49069 Osnabrück

Re: [SIESTA-L] Off-topic: Vesta

[Ricardo Faccio]

Hi Marcos
I think that you procedure is fine. The problem with vesta is that it  
needs yo save changes by step. I mean, first Open your file and remove  
the symmetry, and get a p1 structure. Then save it as a cif file.  
Afyer this read this file and perform the transformation, and save it  
as a different cif file. Finally load it and apply the symmetry, if  
you want, and get another cif file. If you have further problems send  
me your sf and i'll try to check it

Regards
Ricardo


Dr. Ricardo Faccio
Prof. Adj. de Física

Av. Gral. Flores 2124. CC 1157. CP 11800.
Phone: + 598 2 924 9859
Fax: + 598 2 924 1906
Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
-

El 06/04/2011, a las 10:27, Marcos Veríssimo Alves m> escribió:



Hi all,

So, great to know there are knowledgeable people on Vesta in the  
mailing list. My question is the following: I have a cubic  
structure, a perovskite. I have a [sqrt(2) x sqrt(2)] cell of this  
structure, with relaxed positions with rotated oxygen octahedra in  
the x-y plane only, out of which I would like to create a [2 x 2]  
cell. I actually managed to do it (using a xsf file that i created  
from the xyz output), but in a way which I would not call the most  
elegant. It is also a way that is more prone to errors, than I wish  
it were.


The problem is, when one loads an xsf file with the coordinates in  
Vesta, it displays a structure with more atoms than the unit cell  
actually does, and apparently it is the equivalent of XCrysDen's  
conventional cell mode. However, one can choose, in XCrysDen, to  
display only the translational asymmetric unit. This is one thing I  
don't know how to do in Vesta. For a matter of convenience  
(laziness, actually :) ), I have set both PRIMVEC and CONVVEC to the  
cubic lattice vectors, in the xsf file.


Although I have managed to create a [2 x 2] cell, starting from the  
[sqrt(2) x sqrt(2)] using a transformation matrix (easy to deduce),  
I have to eliminate some atoms by setting boundaries to the  
fractional coordinates and checking that the number of atoms is  
actually the expected number. In the case of a [2 x 2] cell, of  
course, we have 4 times as many atoms as in the [1 x 1] cell.  
However, I would be more reassured if there were an automatic way to  
guarantee that the correct number of atoms would be output, instead  
of having to make somewhat extensive checks to ensure this.


Another doubt is about symmetrization of atomic coordinates. If I  
choose a space group for Vesta to symmetrize the atoms' coordinates,  
it ends up creating extra atoms which I can't seem to eliminate - at  
least i don't know the correct way to do it. I have tried the option  
"remove duplicate atoms", but it didn't work. Has anyone run into  
such problems?


If things are not clear, I'll be glad to provide an xsf file to  
illustrate the issues.


Best regards,

Marcos

Re: [SIESTA-L] Off-topic: Vesta

[Marcos Veríssimo Alves]

Hi all,

So, great to know there are knowledgeable people on Vesta in the mailing
list. My question is the following: I have a cubic structure, a perovskite.
I have a [sqrt(2) x sqrt(2)] cell of this structure, with relaxed positions
with rotated oxygen octahedra in the x-y plane only, out of which I would
like to create a [2 x 2] cell. I actually managed to do it (using a xsf file
that i created from the xyz output), but in a way which I would not call the
most elegant. It is also a way that is more prone to errors, than I wish it
were.

The problem is, when one loads an xsf file with the coordinates in Vesta, it
displays a structure with more atoms than the unit cell actually does, and
apparently it is the equivalent of XCrysDen's conventional cell mode.
However, one can choose, in XCrysDen, to display only the translational
asymmetric unit. This is one thing I don't know how to do in Vesta. For a
matter of convenience (laziness, actually :) ), I have set both PRIMVEC and
CONVVEC to the cubic lattice vectors, in the xsf file.

Although I have managed to create a [2 x 2] cell, starting from the [sqrt(2)
x sqrt(2)] using a transformation matrix (easy to deduce), I have to
eliminate some atoms by setting boundaries to the fractional coordinates and
checking that the number of atoms is actually the expected number. In the
case of a [2 x 2] cell, of course, we have 4 times as many atoms as in the
[1 x 1] cell. However, I would be more reassured if there were an automatic
way to guarantee that the correct number of atoms would be output, instead
of having to make somewhat extensive checks to ensure this.

Another doubt is about symmetrization of atomic coordinates. If I choose a
space group for Vesta to symmetrize the atoms' coordinates, it ends up
creating extra atoms which I can't seem to eliminate - at least i don't know
the correct way to do it. I have tried the option "remove duplicate atoms",
but it didn't work. Has anyone run into such problems?

If things are not clear, I'll be glad to provide an xsf file to illustrate
the issues.

Best regards,

Marcos

Re: [SIESTA-L] Off-topic: Vesta

[pietro bonfa]

Hi everybody,
In the last few months I've been playing with Siesta and I found that
both Gdis (CVS version, the stable version lacks of many important
options) and Vesta provide useful and complementary features (Gdis
opens SIESTA fdf files, this is so handy!!).

I hope not to hijack this thread too much but I'd like to ask you one
thing about these programs: I was never able to create a legend
for a crystal structure. Xcrysden labels each atom with its symbol and
produces an acceptable output while the above mentioned tools create
somehow uglier images when labels are added (in my personal opinion).

So the question is: how do you produce a legend with colored atom balls?

Thanks in advances,
cheers,
Pietro



On Wed, Apr 6, 2011 at 12:19 PM, Eric Germaneau  wrote:
>
> Hey Marcos,
>
> I do, it's a great program.
>
> On 04/05/2011 01:46 PM, Marcos Veríssimo Alves wrote:
>
> Hi all,
> This has nothing to do with Siesta, strictly speaking, but it could be of 
> general interest: supercell building.
> I see many people here use and like GDIS. I have tried to download and 
> compile it once, but it didn't compile. With the executable version of GDIS 
> that came with Ubuntu, I found it rather cryptical to use. I feel more 
> comfortable with Vesta, so I would like to know if there are any people 
> knowledgeable in this software here, willing to share a few tips for my 
> specific case? I'll gladly explain it if someone who knows a bit of Vesta is 
> willing to do so :)
> Cheers,
> Marcos
>
> --
> Be the change you wish to see in the world
> — Mahatma Gandhi —
>
> Dr. Éric Germaneau
>
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html

[SIESTA-L] Lipd molecule simulations using SIESTA

[Varrun Ashok]

Dear all,
   I would like to  know if SIESTA can be used to perform energy
calculations on 166 atom based triglyceride molecule. I would like to bring
a metal or metal oxide atom/molecule near a double bond of the triglyceride,
relax the system and find out which metal or metal oxide atom cluster
interacts best with double bond. Is SIESTA a good option to do this? If yes,
How do I go about solving this problem. Could you please suggest some
publications that have done SIESTA simulations for lipids?
Have a nice day!
Regards,
Varrun Ashok