normal Martini Collagen

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2 years 7 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?

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2 years 6 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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1 year 11 months 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.??

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