Cellulose-builder I-beta (110) plane

[Naveen Kumar Vasudevan]

I am conducting all-atom CNC simulations using LAMMPS, In most literature, the surface (110) has been simulated but I used cellulose-builder to obtain my initial structure, the (110) surface is not mentioned in the exposed surfaces. Which surface corresponds to the (110) plane in the monoclinic structure?

 

Command           :  ./cellulose-builder.sh 2 8 6

Input.inp              :  I-BETA, PBC=ALL, PBC_C=TRUE

 

Regards,

Naveen

[Thiago Gomes]

Dear Naveen,

thank you very much for your contact, I beg your pardon for my late response.

For the monoclinic strucuture (i.e. cellulose I-beta) you could get the (110) surface by using, for instance:

Command           :  ./cellulose-builder.sh fibril 6

Input.inp              :  I-BETA, PBC=ALL, PBC_C=TRUE

In the resulting system, the (110) surfaces are the inclined (tilted) ones in Figure 1 in the attached paper.

If you wish to simulate a cristallite with a different cross section and/or exposing larger amounts of (110) surface, I recommend you start with a larger system, say:

Command           :  ./cellulose-builder.sh 4 12 6

Input.inp              :  I-BETA, PBC=ALL, PBC_C=TRUE

and then manually remove unwanted cellulose chains from the resulting PDB file, thus "carving out" and exposing the desired (110) surfaces. VMD should be of much help in selecting which cellulose chains to keep and which to remove.

Please, let me know if that was useful to you and feel free to ask.

Best wishes,

Thiago

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[Marc Ramón]

Dear Dr Gomes,

I am a student working with cellulose.

Like Naveen, I would like to obtain a parallelepiped crystal with (110) and (1-10) crystal planes exposed.

Is there any possibility that you could provide a .tcl file for illustrating the "carving out" method for obtaining the above planes?

Sorry to bother you.

Thank you very much.

Yours sincerely,

Marc R

El martes, 27 de febrero de 2018 a las 18:08:13 UTC+1, Thiago Gomes escribió:

Dear Naveen,

thank you very much for your contact, I beg your pardon for my late response.

For the monoclinic strucuture (i.e. cellulose I-beta) you could get the (110) surface by using, for instance:

Command           :  ./cellulose-builder.sh fibril 6

Input.inp              :  I-BETA, PBC=ALL, PBC_C=TRUE

In the resulting system, the (110) surfaces are the inclined (tilted) ones in Figure 1 in the attached paper.

If you wish to simulate a cristallite with a different cross section and/or exposing larger amounts of (110) surface, I recommend you start with a larger system, say:

Command           :  ./cellulose-builder.sh 4 12 6

Input.inp              :  I-BETA, PBC=ALL, PBC_C=TRUE

and then manually remove unwanted cellulose chains from the resulting PDB file, thus "carving out" and exposing the desired (110) surfaces. VMD should be of much help in selecting which cellulose chains to keep and which to remove.

Please, let me know if that was useful to you and feel free to ask.

Best wishes,

Thiago

2018-02-21 1:17 GMT-03:00 Naveen Kumar Vasudevan <navee...@gmail.com>:

I am conducting all-atom CNC simulations using LAMMPS, In most literature, the surface (110) has been simulated but I used cellulose-builder to obtain my initial structure, the (110) surface is not mentioned in the exposed surfaces. Which surface corresponds to the (110) plane in the monoclinic structure?

 

Command           :  ./cellulose-builder.sh 2 8 6

Input.inp              :  I-BETA, PBC=ALL, PBC_C=TRUE

 

Regards,

Naveen

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