normal Bond and angle for an ionizable lipid

  • dariush
  • dariush's Avatar Topic Author
  • Offline
  • Senior Boarder
More
9 months 3 weeks ago #7766 by dariush
Bond and angle for an ionizable lipid was created by dariush
Hello,

I'd like to know what would be the best parameters (bond and angle) for such a lipid:
www.dropbox.com/s/cphcxwom0xlvf9y/lipid_angle.pdf?dl=0


Here is what I think:

[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.47 1250
3 5 1 0.47 1250
4 6 1 0.47 1250

[angles]
; i j k funct angle force.c.
2 3 5 2 180.0 25.0
3 4 6 2 180.0 10.0

I have another question as well. Do you think the chain length can affect these parameters? Let's say chains are 18:0/18:0.

Thanks!
Dariush

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

More
9 months 1 week ago #7784 by helgi
Replied by helgi on topic Bond and angle for an ionizable lipid
For this one it’s impossible to see except to match to reference atomistic simulations. Also you might want to move the mapping of beads 1 and 2 down one atom (then you can use the default beads/parameters for the tails).

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

Time to create page: 0.092 seconds