Dear all
I would like to solvate a single graphene oxide nanosheet using VMD. As i checked it out it need a psf and a pdb file of the solute. Can everybody help me with this issue?
Hi,
You can build a psf file by using"automatic psf builder " option in "extension" . Hope this helps.
hi Jalil
you should create the pdb file of your solute and then build its psf file with VMD.
OK, you need pdb. file of graphene and sf files, you can follow the tutorials related to Carbon Nanotube on NAMD tutorials, it will help you to make single sheet of graphene oxide, moreover, you will understand how to solvate the structure, important here is to understand the initial structure of your desired simulations. you can follow this link: http://www.ks.uiuc.edu/Training/Tutorials/
Hi dear Sadegh
Appreciated for your consideration. I actually have the pdb file of my solute as you mentioned but my problem is to making the corresponding psf file. Honestly, i could generate the psf file using "animate write psf Go_nano.psf" command but the generated file did not work well at the next step of solvation.
Dear Sayyed,
Would you please tell me the way? I have a solvate and now I like to add graphene sheet to the system? I don't know how to to combine the to things (solvate and graphene sheet) into a single molecule file. Thank you very much!
Best regards,
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