VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Tue Oct 06 2020 - 12:57:28 CDT

Hi Yuvan,

Sometime back I was looking for a MARTINI CG model of silver nanoparticles but couldn't find anything to move forward. There are papers on CG models of gold nanoparticles that you can refer. I believe that 1 to 1 mapping of silver atoms in core will need to be performed. The surface atoms (silver conjugated to ligand) will need to be modelled as one or more CG beads, depending on ligand characteristics. Anyways, I was looking for silver NPs without a ligand and CHARMM-GUI was a big help creating the atomistic structure and I moved on with that without venturing into CG.

Regarding your specific case, I believe that shape based coarse graining available in VMD could be of help.

Another option is to look into scripts that convert graphene/graphite (http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5/physisorption-of-on-graphite) and CNTs and fullerenes (https://github.com/bio-phys/cnt-martini and https://perso.ibcp.fr/luca.monticelli/MARTINI/index.html) to CG models and adopt these, if possible.

Hope this helps a bit.

I believe that others on the mailing list could add further details.

Regards,
Raman

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________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Yuvam Bhateja <yuvamb16_at_gmail.com>
Sent: Tuesday, October 6, 2020 9:47:26 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Silver nanoparticle with coating of protein.

Hello experts.

I am new to VMD and Molecular Dynamics.

I want to build a ligand coated silver nanoparticle. I do not want to go into atomistic calculation and need the composite structure for a coarse grained calculation later.
I think the structure needs to be simulated in water.

Can someone please help what all input files I need and a step by step procedure for constructing these files?
I have build my nanoparticle and obtained the ligand separately.
How can I reduce the no of Atoms in ligand? I obtained it from RCSB PDB.

I'll be highly obliged for any help or guidance.

Regards
Yuvam Bhateja