towhee-users Mailing List for MCCCS Towhee

Dear all,
               I am a  novice user of towhee, I want to perform adsorption
studies of gas on to clay surface using towhee . Can you please suggest me
some insights or  references.


Thanks and regards,
Mohan

Dear Mohan, you will have to get the topology information and assign each of these values (nunit, ntype, vibration, torsion, charge etc.) manually. If your system is really big, it is a good idea to write a script that does this job automatically.

Good luck!

Cheers,
Vikram

Dear all,
               I just started using towhee. I have pdb file for clay
structure, using the utility
I have generated towhee_coords file. In the towhee_input file, there are
some lines as shown below ,


unit ntype
   1 'at    '
vibration
 0
improper torsion
 0
unit ntype
   2 'at    '
vibration
 0
improper torsion
 0
unit ntype
   3 'at    '
vibration
 0
improper torsion
 0
unit ntype
   4 'at    '
vibration
 0
improper torsion
 0
unit ntype
   5 'at    '
vibration
 0
improper torsion
 0
unit ntype
   6 'Si    '
vibration
 0
improper torsion
 0
unit ntype
   7 'Si    '

My question is , do we need to manually edit this input file  and specify
ntype and nunit. or else is there any easier way to do this.

Thanks,
Mohan

Dear all,
               I just started using towhee. I have pdb file for clay
structure, using the utility
I have generated towhee_coords file. In the towhee_input file, there are
some lines as shown below ,


unit ntype
   1 'at    '
vibration
 0
improper torsion
 0
unit ntype
   2 'at    '
vibration
 0
improper torsion
 0
unit ntype
   3 'at    '
vibration
 0
improper torsion
 0
unit ntype
   4 'at    '
vibration
 0
improper torsion
 0
unit ntype
   5 'at    '
vibration
 0
improper torsion
 0
unit ntype
   6 'Si    '
vibration
 0
improper torsion
 0
unit ntype
   7 'Si    '

My question is , do we need to manually edit this input file  and specify
ntype and nunit. or else is there any easier way to do this.

Thanks,
Mohan

Dear Towhee users,

I'm planning to study the solvation patterns of a capped nanoparticle,
which has a ceramic core surrounded by organic molecules (chemically
attached to the ceramic core). The point is that the core is hardly
accessible to the solvent and the organic layer might be conveniently
treated by any regular forcefield (OPLS for instance) and I expect that
this organic layer should play the only relevant role in the interactions
with the solvent, the ceramic core being just an excluded volume and
shape-defining element of my model.

Here comes the issue I'm facing: any standard forcefield which is adequate
for the organic part lacks parameters for the ceramic part (Cd and
inorganic S atoms). I tried to manually edit the towhee_ff_OPLS-aa file to
add Cd atoms (not the Cd2+ ion), replacing one of the carbon atom types
available there, but then I got a huge number of errors while trying to run
towhee, mostly related with missing bonding terms (vibrations, angles and
dihedrals).

One option that apparently worked but I guess it will become a trouble
quite soon is to set the number of vibrations to zero for all atoms
comprising the capped nanoparticle in the towhee_input file, which seems to
work as long as I keep the whole structure still, no MC movement
whatsoever. It works for a single nanoparticle, but eventually I'll be
interested in the interactions between nanoparticles, and then this
approach will become inadequate. It seems to me that it wouldn't work
either using the NPT ensemble, am I right?

Assuming that a fully rigid structure suffices all my needs for the time
being, should I try to write down a customized forcefield with all types of
bonding interactions as dummy interactions (either setting all of them to
"no interaction" or setting the force/energy constants to zero). Would it
be enough to make towhee understand that atoms are bonded and should be
moved as a rigid body?

I did something like that to make towhee accept slightly distorted TIP3P
water molecules from a previous molecular dynamics simulation and it
worked, but I would like to have some advices on maybe some alternative
approach because the capped nanoparticles are quite large, at least 335
atoms.

Any suggestions and comments will be really appreciated!

Thanks in advance.

cheers,

Andre


-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

Thanks, Pascal!

It was indeed a silly error due to my poor understanding on the way Towhee
adds up partial probabilities for a move, it is working now as it should.

cheers,

Andre



On Mon, Mar 17, 2014 at 4:53 PM, Pascal BOULET <pas...@un...>wrote:

> Dear André,
>
> I think that's normal since the probability for moving molecule 2 is zero.
> If you want molecule 2 to move, set for instance the second figure to 0.75;
> then the probability to move it will be 25% (and incidently 25% for the
> last molecule). The probabilities are summing up to 1.
>
> Pascal
>
>
> >-----------------
> Pascal Boulet
> Aix-Marseille University
> MADIREL Laboratory
> Avenue Normandie-Niemen
> 13397 Marseille Cedex 20
> Email: pas...@un...
> Tel. +33 413 55 18 10
> Fax  +33 413 55 18 50
>



-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

Dear André,

I think that's normal since the probability for moving molecule 2 is zero. If you want molecule 2 to move, set for instance the second figure to 0.75; then the probability to move it will be 25% (and incidently 25% for the last molecule). The probabilities are summing up to 1.

Pascal


>-----------------
Pascal Boulet
Aix-Marseille University 
MADIREL Laboratory
Avenue Normandie-Niemen
13397 Marseille Cedex 20
Email: pas...@un...
Tel. +33 413 55 18 10
Fax  +33 413 55 18 50

Hello

tar -xzvf towhee_current.tar.gz

should do it.
type

tar --help
or
man tar

to get more information about tar settings.

Good luck
/Edvin

On 2014-03-12 18:12, William Royle wrote:
>
> I am completely new to the Unix OS and towhee, I have downloaded the 
> towhee file but am struggling to actually open it in the Unix OS. How 
> do I GNU unzip the file? Do I just type in the commands gunzip 
> towhee_current.tar.gz and tar --xf towhee_current.tar?
>
> Will
>
>
>
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I am completely new to the Unix OS and towhee, I have downloaded the towhee
file but am struggling to actually open it in the Unix OS. How do I GNU
unzip the file? Do I just type in the commands gunzip towhee_current.tar.gz
and tar -xf towhee_current.tar?

 

Will



---
This email is free from viruses and malware because avast! Antivirus protection is active.
http://www.avast.com

Hi,
I have a technical question about Towhee capabilities and I appreciate if anybody can give me an answer.
Is it possible to simulate Water droplet condensation on a steel surface when  steel is in contact with a 
supercritical fluid with dissolved water?
In other word, let's say we have SO2+tiny amount of water in supercritical state, from thermodynamic I know 
that this system is single phase and I do not expect water as a separate phase. What if this system be in contact
with a solid phase like steel?

Thank you in advance

Hey Vikram,

I think you can find most information about units here:
http://towhee.sourceforge.net/towhee_ff.html

For energy I think you want to use Kelvin. For distance Angstroms.

Salomon


On Tue, Mar 4, 2014 at 4:40 AM, Ardham Vikram Reddy <ar...@ar...>wrote:

>  Dear Towhee users, I am trying to add the latest Gromos force field to
> Towhee. However, I am unable to find the set of units Towhee uses for
> various parameters. Please let me know if there is any reference manual for
> the same.
>
>
>
> Cheers,
>
> Vikram
>
>
>
>
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-- 
Salomon Turgman Cohen
Assistant Professor
Chemical Engineering
Kettering University
(919) 341-9650

Dear Towhee users, I am trying to add the latest Gromos force field to Towhee. However, I am unable to find the set of units Towhee uses for various parameters. Please let me know if there is any reference manual for the same.

Cheers,
Vikram