normal Create Coarse Grained Carbon Nanotube

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9 years 5 months ago #4134 by SAlih
Dear Martini users and anyone willing help please,

I want to build Coarse Grained for carbon nanotube, I have started to doing it using 6, 4, 2 atoms per a bead. I am using NAMD and VMD, please I wonder if I am doing it right?! As far I know the number of atoms per beads should be equal, is that right??
Is there any way to build it easily please? Because at the moment I am making a cgc file for it and I have to rearrange all atoms in the coordinate (.pdb) file.

Thanks in advance

LILI

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9 years 5 months ago - 9 years 5 months ago #4137 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube
I'm not really up-to-date with cgc files... What's the format?

What do you mean by easily? There isn't an automated topology builder for Martini.

And if you have a mapping and an atomistic conformation, you shouldn't have to "rearrange all atoms in the pdb file".



(please stick to one entry in the forum... No need to flood it with three messages)
Last edit: 9 years 5 months ago by Clement.

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9 years 5 months ago #4141 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
I am using NAMD and VMD. There is an option CG builder from VMD so in order to do that you should have cgc martini file! I have to order all atoms in the coordinates file to make a group of atoms! No I do not have mapping because I am not using gromacs!

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9 years 5 months ago #4143 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube

I am using NAMD and VMD. There is an option CG builder from VMD so in order to do that you should have cgc martini file!


Again: what is the format of a cgc file? What does it describe? Do you have a cgc file defining the Martini force field?

I have to order all atoms in the coordinates file to make a group of atoms! No I do not have mapping because I am not using gromacs!


Mapping is completely independent of the package you use. It's just how you group your atoms. You write it for your own model, gromacs doesn't do it for you.

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9 years 5 months ago #4144 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Sorry I forgot, the format exactly looks like that:
CGBEGIN
CNT SC4 0
CNT C1 0
CNT C2 0
CNT C3 0
CNT C4 0
CNT C5 0
CNT C6 0
CNT C7 0
CNT C8 0
CGEND

CGBEGIN
CNT SC4 0
CNT C9 0
CNT C10 0
CNT C11 0
CNT C12 0
CNT C13 0
CNT C14 0
CNT C15 0
CNT C16 0

CGBEGIN
CNT SC4 0
CNT C17 0
CNT C18 0
CNT C19 0
CNT C20 0
CNT C21 0
CNT C22 0
CNT C23 0
CNT C24 0
CGEND

CGBEGIN
CNT SC4 0
CNT C25 0
CNT C26 0
CNT C27 0
CNT C28 0
CNT C29 0
CNT C30 0
CNT C31 0
CNT C32 0
CGEND

CGBEGIN
CNT SC4 0
CNT C33 0
CNT C34 0
CNT C35 0
CNT C36 0
CNT C37 0
CNT C38 0
CNT C39 0
CNT C40 0
CGEND

CG database file format

The current bead definition database format (which is subject to change) is a single file with a set of one or more bead blocks, each of which starts with a CGBEGIN statement and ends with a CGEND statement. Any lines outside of a CGBEGIN ... CGEND block will be ignored, as will blank lines or lines starting with a # character. Each line within a bead block contains three whitespace delimited pieces of information: A residue name, atom name, and resid offset (relative to that of the key atom). The first line in the block contains the information that will be applied to the newly created CG bead, the second line of the block is the "key" atom, which will be used to identify clusters of atoms that should be turned into a bead, and all subsequent lines are component atoms of the bead. Note that one bead will be created for each key atom found (unless it has been previously incorporated into another bead), but that missing component atoms will be ignored.


The cgc is how you group atoms.

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9 years 5 months ago #4145 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube
I see! Great. Then I suggest you try on different mappings, starting with something close to 3 carbons to 1 SC4 bead (by the way, check the initial paper, but S beads are for 2:1 or 3:1 mapping only; you have to use regular beads, e.g. C4 if that's what you want, for higher mappings). Then you can move to more complicated mappings maybe, depending on the properties you want to reproduce and what you obtain.

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9 years 5 months ago #4146 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Thanks a lot I will try to make a cgc file for the whole structure. SC4 particle type describe a carbon particle with hydrophobic properties if im right!
Again I have a pdb file, so should I rearrange them to group them or doe doesn't need it please? for example the atoms like that:

ATOM 1 C CNT X 1 -6.270 1.208 8.748 0.00 0.00 CCC C
ATOM 2 C CNT X 2 -6.825 2.298 8.039 0.00 0.00 CCC C
ATOM 3 C CNT X 3 -7.690 3.162 8.748 0.00 0.00 CCC C
ATOM 4 C CNT X 4 -8.780 3.718 8.039 0.00 0.00 CCC C
ATOM 5 C CNT X 5 -9.988 3.909 8.748 0.00 0.00 CCC C

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9 years 5 months ago #4149 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube

Thanks a lot I will try to make a cgc file for the whole structure.


Shouldn't be too complicated indeed.

SC4 particle type describe a carbon particle with hydrophobic properties if im right!


You're indeed right. A small hydrophobic particle though, hence the "S" prefixing it. Same for (S)C1, (S)C2, (S)C3, and (S)C5 as well, make sure you have the right properties reproduced. (S)C4 is just one type of hydrophobicity, might not be optimal for what you want to do.

Again I have a pdb file, so should I rearrange them to group them or doe doesn't need it please? for example the atoms like that:

ATOM 1 C CNT X 1 -6.270 1.208 8.748 0.00 0.00 CCC C
ATOM 2 C CNT X 2 -6.825 2.298 8.039 0.00 0.00 CCC C
ATOM 3 C CNT X 3 -7.690 3.162 8.748 0.00 0.00 CCC C
ATOM 4 C CNT X 4 -8.780 3.718 8.039 0.00 0.00 CCC C
ATOM 5 C CNT X 5 -9.988 3.909 8.748 0.00 0.00 CCC C


I have no idea what you use to do that! Again, I'm not familiar with the tools you use. I would write a small script to generate your CG structure from your atomistic one, taking the center of masses of all the atoms of each bead as initial coordinates for your CG beads. For the topology (bonded parameters) I guess you have to write it by yourself.

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9 years 5 months ago #4150 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Thanks a lot, I think I have to rename c in the pdb file into c1, c2, c3......c320 in order to make cgc file. Yes its not so complicated though.
I am a little bit confused about type of the particle, for nano particles they have been using SC4, I to simulate it with POPC for checking the interactions and might be for elasticity properties! Could you please explain what exactly you mean?!

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9 years 5 months ago #4153 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube
Check the Martini papers again!

C particles are hydrophobic at various levels. C1 is extremely hydrophobic, C5 much less. You choose the particle type(s) for which the properties you're parameterizing your CNT against are best reproduced. Typically, Martini is built around partition free energies, so you should try to reproduce this; if available. Otherwise there's a bunch of other properties you can check, your choice, but you should try to stay within the boundaries of the Martini philosophy. Anyway, you might discover that in your case SC4 might be the best compromise, OR NOT. It's your job to test that. And depending on your mapping (~4:1 or ~2:1), regular or S beads should be used.

Defining a mapping isn't only about grouping atoms together! The bead types needs to be tweaked too.

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9 years 5 months ago #4160 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Thanks a lot, I will do it as you advised me, but I want to maintain geometry of carbon nanotube and I guess I do not have to use SC4 at all. I have to use C and I should check which one C1,C2,C3,C4 or C5!
I have changed C into C1, C2, C3....C320, but it took me all the day yesterday. It should be some scripts to change lines in the pdb files through VMD, do you know any of this script please?

Thanks again for all advises and it helped a lot.

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9 years 5 months ago #4162 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube
When you say "maintain the geometry", you can be referring to added constraints, or to the geometry of your initial conformation; be careful in your wording.

Again, I don't what type(s) of bead you "should" use; it depends on your mapping...

As for your last question about changing the names, you can use a small shell script or whatever... Quite easy to do with sed or similar. VMD is just a graphical tools, quite hard to use for small details like this.

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9 years 5 months ago #4166 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Thanks a lot.
About parametrization how can I be sure use the correct one please?

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9 years 5 months ago #4167 by Clement

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9 years 4 months ago #4175 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Thanks a lot!
There is a topology file in the following link:
perso.ibcp.fr/luca.monticelli/MARTINI/index.html
I do not know Gromacs, .itp files are the parameter files or just structures and topologies please?

If so I can make parameter file for my CG CNT based on the AA and using the above link to parametrize CNT!

Thanks a lot

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9 years 4 months ago #4176 by Clement
Replied by Clement on topic Create Coarse Grained Carbon Nanotube
http://www.gromacs.org/Documentation/File_Formats

Structure files are .gro or .pdb for instance. Among others.

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9 years 4 months ago #4181 by SAlih
Replied by SAlih on topic Create Coarse Grained Carbon Nanotube
Thanks a lot.

Should the number of atoms per particles in all CNT are to be equal? I mean for example one particle has 3 atoms (3:1) and others should be have the same number of atoms please in the CNT? I have made CG for all structure but it looks not good!
Thanks

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