normal System setup with amphipol A8-35 polymer

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
1 year 4 months ago #5751 by almeida
almeida created the topic: System setup with amphipol A8-35 polymer
Hi all,

I want to run a simulation of a membrane protein with amphipol A8-35 polymer, similar to the work 10.1007/s00232-014-9690-8.

I have a new .itp file for A8-35 and I want to add different amounts of the A8-35 molecules randomly positioned in the simulation box, as part of the solvent.

Any idea about how to do it?

Thanks in advance

Yasser

Please Log in or Create an account to join the conversation.

More
1 year 4 months ago #5752 by mnmelo
mnmelo replied the topic: System setup with amphipol A8-35 polymer
Hi Yasser,

I suggest you follow the same procedure as we describe in the bilayer self-assembling tutorial , but instead of randomly placing lipids, you randomly place your polymer.

Good luck and let us know how it goes,
Manel

Please Log in or Create an account to join the conversation.

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
1 year 4 months ago #5755 by almeida
almeida replied the topic: System setup with amphipol A8-35 polymer
Thanks!

In my case I don't have a .gro file for A8-35. I tried to run molmaker.py to convert the .itp to .gro but the script doesn't contains the martini ff.
Any idea how to convert .itp to CG .gro?

Please Log in or Create an account to join the conversation.

More
1 year 4 months ago #5756 by mnmelo
mnmelo replied the topic: System setup with amphipol A8-35 polymer
Indeed molmaker.py is the way to go. If you download the martini definition file and place it in the same directory, then pass the option
-ff martini_v2.2.itp
to molmaker.

Note that I'm linking to the Martini 2.2 version. This should be what you need, but do check if other versions suit your purpose better.

Please Log in or Create an account to join the conversation.

  • almeida
  • almeida's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
1 year 4 months ago #5757 by almeida
almeida replied the topic: System setup with amphipol A8-35 polymer
It works!

Thanks

Please Log in or Create an account to join the conversation.

Time to create page: 0.085 seconds