×
Welcome to the Kunena forum!
Tell us and our members who you are, what you like and why you became a member of this site.
We welcome all new members and hope to see you around a lot!
Tell us and our members who you are, what you like and why you became a member of this site.
We welcome all new members and hope to see you around a lot!
MCF file
- Ojaghlou
-
Topic Author
- Offline
- New Member
-
Less
More
- Posts: 7
- Thank you received: 1
8 years 8 months ago #40
by Ojaghlou
Hello everyone,
I am trying to simulate the confined water between two graphene sheets in GCMC ensemble. I knew how to create the MCF file for water but I don't have any Idea to make the MCF file for graphene sheets. should I create another box for each graphene sheet?
Should I only use the unit cell of graphene in order to make a pdb file?
I would appreciate if anybody can help me.
Thank you,
Neda
I am trying to simulate the confined water between two graphene sheets in GCMC ensemble. I knew how to create the MCF file for water but I don't have any Idea to make the MCF file for graphene sheets. should I create another box for each graphene sheet?
Should I only use the unit cell of graphene in order to make a pdb file?
I would appreciate if anybody can help me.
Thank you,
Neda
Please Log in to join the conversation.
- ryangmullen
-
- Offline
- Administrator
-
Less
More
- Posts: 124
- Karma: 4
- Thank you received: 24
- Ojaghlou
-
Topic Author
- Offline
- New Member
-
Less
More
- Posts: 7
- Thank you received: 1
- ryangmullen
-
- Offline
- Administrator
-
Less
More
- Posts: 124
- Karma: 4
- Thank you received: 24
8 years 6 months ago #62
by ryangmullen
Hi Neda,
There are several examples of simulating various fluids within a rigid model of silicalite. You can find the examples in the Examples/GCMC directory. Each of these examples begins with an empty zeolite. During the course of the simulation, fluid phase molecules (e.g. methane, butane, nitrogen) are inserted according to the chemical potential set point.
See Ch 6 of the user guide for information on what files you will need to simulate water between sheets of graphene.
Do you have a configuration file listing your graphene atom coordinates?
There are several examples of simulating various fluids within a rigid model of silicalite. You can find the examples in the Examples/GCMC directory. Each of these examples begins with an empty zeolite. During the course of the simulation, fluid phase molecules (e.g. methane, butane, nitrogen) are inserted according to the chemical potential set point.
See Ch 6 of the user guide for information on what files you will need to simulate water between sheets of graphene.
Do you have a configuration file listing your graphene atom coordinates?
Please Log in to join the conversation.
- ryangmullen
-
- Offline
- Administrator
-
Less
More
- Posts: 124
- Karma: 4
- Thank you received: 24
- Ojaghlou
-
Topic Author
- Offline
- New Member
-
Less
More
- Posts: 7
- Thank you received: 1
8 years 6 months ago #69
by Ojaghlou
Thanks for your reply. No, I am still working on it.
before I started MC, I was working in MD. I made the configuration with VMD and I used Lammps and I didn't have any problem. But now I am confused. How can I add graphite sheets to my system?
Should I use the new box system?1 box for water and 1 box for graphite sheets?
Or I should use fragment and built graphite sheet and then use the fragment in my main script.
I am still reading Ch6 and working on examples to understand.
Please help me in this part.
Thanks, Neda
before I started MC, I was working in MD. I made the configuration with VMD and I used Lammps and I didn't have any problem. But now I am confused. How can I add graphite sheets to my system?
Should I use the new box system?1 box for water and 1 box for graphite sheets?
Or I should use fragment and built graphite sheet and then use the fragment in my main script.
I am still reading Ch6 and working on examples to understand.
Please help me in this part.
Thanks, Neda
Please Log in to join the conversation.
Time to create page: 0.123 seconds