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create topology file for CNT
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9 years 6 months ago #4136
by SAlih
create topology file for CNT was created by SAlih
Can anyone help to make a topology file for CG carbon nanotube please?
Thanks
Thanks
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9 years 6 months ago - 9 years 6 months ago #4138
by Clement
Replied by Clement on topic create topology file for CNT
We could indeed help, but we might need more information... What did you try, what did you do so far, what's the goal of the model, ...?
(please stick to one entry in the forum... No need to flood it with three messages)
(please stick to one entry in the forum... No need to flood it with three messages)
Last edit: 9 years 6 months ago by Clement.
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9 years 6 months ago #4140
by SAlih
Replied by SAlih on topic create topology file for CNT
Thanks for the reply, I have a pore carbon nano tube "zigzag (10, 0) with a diameter (7.82 Ao) and relatively short 30 Angstroms, 320 atoms". I am using NAMD and VMD, I have started to make a CG for it. I have grouped 8 atoms into a bead. At the moment I have done for just 40 atoms. I need to have a topology file for it. I want to simulate with membrane POPC.
First I want to finish all group of atoms into bead. Then make cgc file as required by VMD, I have done it for 8 group, So now I have cg coordinates for this 8 group. So I want to use PSFgen package to make a psf file or using Autopsf from VMD. SO to make a psf I need a topology file!
Thanks
First I want to finish all group of atoms into bead. Then make cgc file as required by VMD, I have done it for 8 group, So now I have cg coordinates for this 8 group. So I want to use PSFgen package to make a psf file or using Autopsf from VMD. SO to make a psf I need a topology file!
Thanks
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9 years 6 months ago - 9 years 6 months ago #4142
by Clement
Awesome.
I understand. 8 atoms are starting to be way too much... especially for ring-like structure, 2 to 3 atoms per (S) bead should be more optimal. Look at the structures of the nano-particles parameterized by Monticelli et al. available on the website you mentioned in another post. Phenyl groups are for instance modeled by 3 beads to keep information about planarity. But in your case it might not be primordial, so maybe you can look into other mappings... But try to limit it to 4 (5 in last resort) non-hydrogen atoms per bead.
I bet you do. Anyway, what are you expecting from us? We can help for this, but not make it for you... Start with an educated guess looking at topologies for similar compounds, build your topology for a specific mapping, try it on with smaller residues, ... the usual.
One last thing: we are generally more used to the formats used by gromacs, but you can always ask, we will try our best. But don't expect an immediate answer then, we need to check manuals and whatnot to avoid sending you the wrong way. But the way of thinking and defining things for Martini is the same whatever package you use!
Good luck!
Replied by Clement on topic create topology file for CNT
I have a pore carbon nano tube "zigzag (10, 0) with a diameter (7.82 Ao) and relatively short 30 Angstroms, 320 atoms".
Awesome.
I am using NAMD and VMD, I have started to make a CG for it. I have grouped 8 atoms into a bead. At the moment I have done for just 40 atoms. I need to have a topology file for it.
I understand. 8 atoms are starting to be way too much... especially for ring-like structure, 2 to 3 atoms per (S) bead should be more optimal. Look at the structures of the nano-particles parameterized by Monticelli et al. available on the website you mentioned in another post. Phenyl groups are for instance modeled by 3 beads to keep information about planarity. But in your case it might not be primordial, so maybe you can look into other mappings... But try to limit it to 4 (5 in last resort) non-hydrogen atoms per bead.
First I want to finish all group of atoms into bead. Then make cgc file as required by VMD, I have done it for 8 group, So now I have cg coordinates for this 8 group. So I want to use PSFgen package to make a psf file or using Autopsf from VMD. SO to make a psf I need a topology file!
I bet you do. Anyway, what are you expecting from us? We can help for this, but not make it for you... Start with an educated guess looking at topologies for similar compounds, build your topology for a specific mapping, try it on with smaller residues, ... the usual.
One last thing: we are generally more used to the formats used by gromacs, but you can always ask, we will try our best. But don't expect an immediate answer then, we need to check manuals and whatnot to avoid sending you the wrong way. But the way of thinking and defining things for Martini is the same whatever package you use!
Good luck!
Last edit: 9 years 6 months ago by Clement.
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