[gmx-users] REPOST Coarse graining carbon nanotubes and MARTINI

[Peter Kroon]

Hi Raman,


I forwarded your question to some people off list, and chance has it I
just got a reply back! So with a big thanks to R. Alessandri and M. Vögele!


Peter



Hi,

1.) 
We made a tool to create Martini models for open carbon nanotubes: 
https://github.com/bio-phys/cnt-martini.
The parameters are described in the following paper:
http://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00011e
For closed/capped CNTs, check out the work by Luca Monticelli:
http://perso.ibcp.fr/luca.monticelli/MARTINI/index.html

2.) 
I have never used VMD for coarse-graining, but I would refrain from
using residue-based methods, as they are very specific for proteins and
will not work for other types of molecules.

Best regards,
Martin

-- 

Martin Vögele, M.Sc.
Max Planck Institute of Biophysics
Department of Theoretical Biophysics
Max-von-Laue-Str. 3
D-60438 Frankfurt am Main
Tel. +49 (0)69 / 6303 2505 


On 12-07-18 14:31, Raman Preet Singh wrote:
> Dear All,
>
> I have earlier posted the below email but received no reply. I am reposting it and will be thankful if someone can help me out.
>
> Regards,
> Raman
>
>
> On Jul 6, 2018 3:02 PM, Raman Preet Singh <ramanpreetsingh at hotmail.com> wrote:
>> Dear All,
>>
>>
>> I want to run a CG simulation of carbon nanotubes (CNTs) and different proteins. I have a few questions for which I request help:
>>
>>   1.
>> Several groups have used CG models of CNTs, mapping 2, 2.5 or 3 carbons per CG bead. I am a novice in CG models. Any help on creating CG models or reference to a tutorial/website/paper/script will be appreciated.
>>   2.
>> VMD offers a residue-based CG which can convert the atomistic to CG structure of proteins. Will it be OK to use this CG model of protein with CG model of CNTs and perform simulation using MARTINI force field.
>>
>>
>> Thank you in advance.
>>
>>
>> Regards,
>>
>> Raman
>>
>>
>>
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