- Posts: 10
Martini Collagen
- Jingjie Yeo
-
Topic Author
- Offline
- Fresh Boarder
Less
More
7 years 8 months ago #5777
by Jingjie Yeo
Martini Collagen was created by Jingjie Yeo
Hi everyone, I've been trying to model multiple strands of the same collagen as in the original paper:
DOI: 10.1021/ct100015v
So far I've only managed to run it in NPT up to about a couple of million steps before the system explodes ("atom moved too far apart" errors). I'm using the Martini22p forcefield with Gromacs 5 and the latest .mdp options from the Martini website.
I've tried reducing the timestep to 10fs to no avail. I've also tried increasing the -rdd option in mdrun which helped a little but does not resolve this issue. Has anyone else encountered this problem before?
DOI: 10.1021/ct100015v
So far I've only managed to run it in NPT up to about a couple of million steps before the system explodes ("atom moved too far apart" errors). I'm using the Martini22p forcefield with Gromacs 5 and the latest .mdp options from the Martini website.
I've tried reducing the timestep to 10fs to no avail. I've also tried increasing the -rdd option in mdrun which helped a little but does not resolve this issue. Has anyone else encountered this problem before?
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
7 years 8 months ago #5839
by xavier
Replied by xavier on topic Martini Collagen
Yes, this unfortunately happens ... where does your system explodes? GMX should tell you where the system fails ...
Please Log in or Create an account to join the conversation.
- gupta.rakesh2
-
- Offline
- Fresh Boarder
Less
More
- Posts: 5
7 years 4 days ago #7238
by gupta.rakesh2
Replied by gupta.rakesh2 on topic Martini Collagen
I am also facing the similar problem.
Could you please tell me how did you solve the problem.??
Could you please tell me how did you solve the problem.??
Please Log in or Create an account to join the conversation.
Time to create page: 0.095 seconds