towhee-users Mailing List for MCCCS Towhee

Hi Ella:

I'm actually trying to do something similar, only with water around a 
frozen protein
(but with the protein still interacting with the water).  Since you still 
want the Au to interact
with the organic layer, but not get moved, I think the easiest modification 
would be to hack the main
loop so that Au never gets chosen for trial moves in the first place.  This 
is better anyway for an energy
accounting standpoint (so you can compare total energies from simulations 
with and without your modifications).

If you look at the code for each of the movetypes, they begin with a line
       rchain  = twh_random()
(this was from line 65 of tranatom.F)

So if you can figure out what chain #(s) your AU's are (just add some WRITE 
statements  in writeaverages.F
which is what generates all the text at the end of the run, for example) 
you could either
modify the beginning of each movetype you are using to exclude Au "chains"
(if you are only using translate and rotate moves like me then it's just 
rotate.F, tranatom.F, trancom.F).  If you are using alot
of movetypes it might be easier to make a single change in random.F so that 
it keeps re-generating a random number until the output would not be an AU 
"chain" .

Hope it helps - let us know if it works out!

Alan

At 07:10 PM 10/31/2005 +0000, ella gale wrote:
>Hello,
>
>I am trying to minimise a system that consists of a metal surface (Two
>layers of a gold crystal) and an organic layer attached to it, using
>CBMC (configurational-bias Monte Carlo) at a low temperature (10K). I
>want to minimise the organic layer but not move any of the gold atoms at
>all. To do this I have altered a copy of the towhee_ff_UFF forcefeild
>file to make all the gold bonds a fixed bond length to prevent the gold
>from rearranging. I removed the angle interaction between gold atoms,
>but could not see a way of removing Au-Au pair potentials (I want the
>pair potential interactions between the gold surface and the organic
>layer). When I run it the gold atoms are seen to have moved at the end
>of the minimisation.
>
>Is there a way to do CBMC only on the organic layer? Or to freeze the
>gold atoms in place during the minimisation? Or a way to turn off
>Gold-Gold pair potentials? I think that this is what is causing my gold
>atoms to move.
>
>Any help would be appreciated.
>
>Ella Gale

Hello,

I am trying to minimise a system that consists of a metal surface (Two
layers of a gold crystal) and an organic layer attached to it, using
CBMC (configurational-bias Monte Carlo) at a low temperature (10K). I
want to minimise the organic layer but not move any of the gold atoms at
all. To do this I have altered a copy of the towhee_ff_UFF forcefeild
file to make all the gold bonds a fixed bond length to prevent the gold
from rearranging. I removed the angle interaction between gold atoms,
but could not see a way of removing Au-Au pair potentials (I want the
pair potential interactions between the gold surface and the organic
layer). When I run it the gold atoms are seen to have moved at the end
of the minimisation.

Is there a way to do CBMC only on the organic layer? Or to freeze the
gold atoms in place during the minimisation? Or a way to turn off
Gold-Gold pair potentials? I think that this is what is causing my gold
atoms to move.

Any help would be appreciated.

Ella Gale

Hello towhee-users,

A few towhee-related items in this email.

First, some shameless self promotion.  I will be giving the following 
Towhee related talk at the AIChE Annual meeting in Cincinnati on Monday 
Oct. 31, 2005
#87 - Thermodynamic Properties and Phase Behavior: Part I (01A02)
Computing Vapor-Liquid Coexistence Curves for Metals
Marcus Martin, Multiscale Computational Materials Methods, Sandia 
National Laboratories, PO Box 5800 Mail Stop 1110, Albuquerque, NM 
87185-1110

Vapor-liquid coexistence curves are computed for metallic elements 
using the Towhee Monte Carlo molecular simulation package. Results are 
presented for several Embedded-Atom Method models of iron and for some 
Stillinger-Weber models of silicon. Deviations from the law of 
rectilinear diameters are observed over a significant temperature 
range, and a more complex set of equations for fitting coexistence 
densities is utilized to predict critical points. Finally, the highly 
non-ideal vapor pressures serve as a good test of the of the 
thermodynamic and virial methods for computing the pressure, and the 
relative merits of these two methods are discussed.

Second, related to the above, as a substantial fraction of the Towhee 
development, debugging support, manual, and coding teams will be at the 
AIChE meeting next week, and another meeting the following week, the 
email support will be sporadic at best.  I will begin wading through 11 
days of email again on November 10 so please be patient when expecting 
a response until that time.

Third, if any of you wish to self-identify as giving a Towhee related 
presentation please send me an email and I will add it to the list on 
the Towhee web page.
http://towhee.sourceforge.net/towhee_presentations.html

thank you,

Marcus

-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net


-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net

On Oct 21, 2005, at 10:28 AM, Niels Hansen wrote:
> I try to reproduce some simulation results from the literature, for 
> example vapor-liquid equilibria for H2S using a Lennard-Jones plus 
> point charge model. Almost always the Ewald sum is used with tinfoil 
> boundary conditions. Do I use tinfoil boundary conditions in towhee 
> when I set the "dielect"-variable to 1.0?

Towhee uses the tinfoil boundary conditions in combination with the 
Ewald sum all of the time.

The dielect variable just changes the dielectric constant for the 
coulombic interactions.  It is essentially equivalent to scaling all of 
the charges in the system by 1/dielect.

Marcus
-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net

Dear all,

I try to reproduce some simulation results from the literature, for 
example vapor-liquid equilibria for H2S using a Lennard-Jones plus point 
charge model. Almost always the Ewald sum is used with tinfoil boundary 
conditions. Do I use tinfoil boundary conditions in towhee when I set 
the "dielect"-variable to 1.0?

Many thanks,

Niels

On Oct 13, 2005, at 6:38 AM, Niels Hansen wrote:
> I am simulating binary mixtures in the Gibbs-NPT ensemble. When I 
> compared the input pressure with the viriral pressure in the output 
> file I noticed that the latter is slightly smaller. I wonder what 
> pressure I should use to plot a P-x diagram, the input pressure or the 
> virial pressure ?

I would use the input pressure.  However, a vapor phase virial pressure 
is normally a very good estimate.  You might want to check the 
pressurefreq variable to make sure it is set relatively low ( in the 1 
to 10 range) so that you are taking a reasonable number of pressure 
measurements into the average.

If they still differ then please submit a bug report with the files so 
I can track this down.

thanks,

Marcus

-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net


-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net

Dear all,

I am simulating binary mixtures in the Gibbs-NPT ensemble. When I 
compared the input pressure with the viriral pressure in the output file 
I noticed that the latter is slightly smaller. I wonder what pressure I 
should use to plot a P-x diagram, the input pressure or the virial 
pressure ?

Thank you,

Niels Hansen

On Oct 12, 2005, at 10:03 AM, ella gale wrote:
> simulation) a surface using towhee. What I want to do is implement
> periodic boundary conditions round a unit cell of the surface such that
> the bonds can go across the boundary, and intermolecular forces are 
> felt
> from across the boundary. (In other words pretty standard periodic
> boundary conditions). How is this done in towhee? At the moment I am
> including bonds across the boundary in the input file and using
> towhee_cell to give the input cell. Is this enough?

Towhee properly handles molecules that span the periodic boundaries.  
You will still need to make sure that your molecule input file has all 
of the appropriate bonded interactions.  I think that the towhee_coords 
would be more appropriate in that case as you set up your entire 
surface as a single molecule making sure that you have all of the bonds 
in the proper positions.

The Catlow_Zeolite_4a example has a bonded solid structure that spans 
the periodic boundaries.

On Oct 12, 2005, at 11:15 AM, Alan Chen wrote:
> "coulombstyle" keywords and the "classical potential" (i.e. Lennard 
> Jones) keywords.
> Your choices are ewald or minimum image for the former, and you can 
> have shift functions,
> tail corrections, and cutoffs for the latter.  Personally, I always 
> use minimum image when in doubt, but that's just me (of course it's 
> the slowest since it doesn't use cutoffs).

Minimum image is not a good choice for general simulations.  It is 
implemented mainly for single molecule in gas phase simulations.  You 
can get some weird effects using minimum image that are related to 
simulation box shape.

The Ewald sum is the best general choice for coulombics in Towhee.

Marcus

-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net

Hi Ella:

To the best of my knowledge PBC are always on.  You do need to choose
how you want to treat long and short range interactions, through the
"coulombstyle" keywords and the "classical potential" (i.e. Lennard Jones) 
keywords.
Your choices are ewald or minimum image for the former, and you can have 
shift functions,
tail corrections, and cutoffs for the latter.  Personally, I always use 
minimum image when in doubt, but that's just me (of course it's the slowest 
since it doesn't use cutoffs).

See the input manual at
http://towhee.sourceforge.net/input/towhee_input_v4_12_x.html
for more details.

Cheers,
Alan




At 05:03 PM 10/12/2005 +0100, you wrote:
>Hi everyone,
>
>I'm interested in minimizing (by doing a low temperature Monte Carlo
>simulation) a surface using towhee. What I want to do is implement
>periodic boundary conditions round a unit cell of the surface such that
>the bonds can go across the boundary, and intermolecular forces are felt
>from across the boundary. (In other words pretty standard periodic
>boundary conditions). How is this done in towhee? At the moment I am
>including bonds across the boundary in the input file and using
>towhee_cell to give the input cell. Is this enough?
>
>Any help would be greatly appreciated, as ever.
>
>Thank you
>
>Ella Gale

Hi everyone,

I'm interested in minimizing (by doing a low temperature Monte Carlo
simulation) a surface using towhee. What I want to do is implement
periodic boundary conditions round a unit cell of the surface such that
the bonds can go across the boundary, and intermolecular forces are felt
from across the boundary. (In other words pretty standard periodic
boundary conditions). How is this done in towhee? At the moment I am
including bonds across the boundary in the input file and using
towhee_cell to give the input cell. Is this enough?

Any help would be greatly appreciated, as ever.

Thank you

Ella Gale

Dear Prof Marcus Martin,
 
I found that the value will be replaced by ******** if the value is beyond 1000 in the towhee_movie, that means that the maximum of the box length should be less than 1000 angstrom. I checked the preproc.h, there is no option to modify the box length. Since I am simulating the colloid phase transitions, is it possible to make the box length larger than 1000 angstrom and how to modify it?  
Many thanks,
 
Li JG
Department of chemical engineering
National University of Singapore

Marcus Martin <ma...@sa...> wrote:
On Oct 6, 2005, at 5:29 AM, li jianguo wrote:
> the radial distribution function. I got error message
> as follows:
> Would you like to enter different cutoff values?
> (T/F)
> F
> bad repetition count: incomprehensible list input
> apparent state: unit 10 named towhee_movie
> last format: list io
> lately reading direct formatted external IO
> Aborted
>
> I checked the file-towhee_movie and found there are
> some numbers replaced by **********, can anybody tell
> me what is the possible reason and how to fix it?

Some values must have exceeded the formatting. Send the file to 
towhee-bugs and we'll take a look.

Marcus
-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net


-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net




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On Oct 7, 2005, at 12:51 AM, li jianguo wrote:
> By the way, if I want to send files to towhee-bugs, which email 
> address should I use? Is it tow...@li... ?

The address for all bug reports is
tow...@li...

Marcus

-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net

Dear Prof Marcus Martin,
 
Thanks for your reply. I am simulating phase transitions of colloids consisting of several beads, so I construct a fake molecule. In order to fix the bond and angle, I set the value of bond and angle constant to be very high, so in the output file, a warning appeared saying that bend vib energy is too high. Is the ******** in the towhee_movie  is because of this?
By the way, if I want to send files to towhee-bugs, which email address should I use? Is it tow...@li... ?
 
Many thanks,
Li JG
Department of chemical engineering
National University of Singapore

Marcus Martin <ma...@sa...> wrote:
On Oct 6, 2005, at 5:29 AM, li jianguo wrote:
> the radial distribution function. I got error message
> as follows:
> Would you like to enter different cutoff values?
> (T/F)
> F
> bad repetition count: incomprehensible list input
> apparent state: unit 10 named towhee_movie
> last format: list io
> lately reading direct formatted external IO
> Aborted
>
> I checked the file-towhee_movie and found there are
> some numbers replaced by **********, can anybody tell
> me what is the possible reason and how to fix it?

Some values must have exceeded the formatting. Send the file to 
towhee-bugs and we'll take a look.

Marcus
-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net


-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net




-------------------------------------------------------
This SF.Net email is sponsored by:
Power Architecture Resource Center: Free content, downloads, discussions,
and more. http://solutions.newsforge.com/ibmarch.tmpl
_______________________________________________
Towhee-users mailing list
Tow...@li...
https://lists.sourceforge.net/lists/listinfo/towhee-users




		
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On Oct 6, 2005, at 5:29 AM, li jianguo wrote:
> the radial distribution function. I got error message
> as follows:
>  Would you like to enter different cutoff values?
> (T/F)
> F
> bad repetition count: incomprehensible list input
> apparent state: unit 10 named towhee_movie
> last format: list io
> lately reading direct formatted external IO
> Aborted
>
> I checked the file-towhee_movie and found there are
> some numbers replaced by **********, can anybody tell
> me what is the possible reason and how to fix it?

Some values must have exceeded the formatting.  Send the file to 
towhee-bugs and we'll take a look.

Marcus
-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net


-------------------------------------------------------------------
Marcus G. Martin
Senior Member of Technical Staff
Multiscale Computational Materials Methods
Sandia National Laboratories
PO Box 5800 MS 1110
Albuquerque NM 87185-1110
v. 505 284-6355
f. 505 845-7442
http://www.cs.sandia.gov/marcusmartin/
http://towhee.sourceforge.net

Dear all,

I am simulating the phase diagram of colloids, I met
problems when using analyse_movie utility to calculate
the radial distribution function. I got error message
as follows:
[lijianguo@frontend-0 210]$ analyse_movie.x
 Opening towhee_movie
 towhee_movie input version  2
 Please answer the questions T (true) or F (false)
 Compute intermolecular radial distribution functions?
(T/F)
T
 Input number of bins for rdf
100
 Amount of additional displacement (0.0 for none).
0.0
 The current cut-offs used to compute rdf in each
 box are   250.  250.
 Would you like to enter different cutoff values?
(T/F)
F
bad repetition count: incomprehensible list input
apparent state: unit 10 named towhee_movie
last format: list io
lately reading direct formatted external IO
Aborted

I checked the file-towhee_movie and found there are
some numbers replaced by **********, can anybody tell
me what is the possible reason and how to fix it?

Thanks a lot,

Li JG
Department of chemical engineering
National University of Singapore




		
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Dear all,
 
I am simulating the phase equilibrium of colloid particles by Towhee, in the final configuration, I found some of the particles associate and formed several clusters. Is there any paramter that can characterize the degree of the particle association? I thougt of radial distribution function, is there any other parameters?
Thanks a lot,
 
Li JG
Department of chemical engineering
National University of Singapore



		
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