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Martini Collagen
- Jingjie Yeo
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7 years 9 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?
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- xavier
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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 ...
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- gupta.rakesh2
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7 years 2 weeks 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.??
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