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normal An error with rdd

  • dujiangfeng
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11 years 4 months ago #1302 by dujiangfeng
An error with rdd was created by dujiangfeng
Dear All,

I let my protein-membrane system run for a 10 micro seconds but it was a pity when the simulation at the time 273 ns, an error happened: "1 of the XXXX bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm)".
I think I understand this problem, and I also can find which atoms actually they are. But I don't know how to figure it out. I really appreciate if anyone can help.

Sjeng.

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11 years 4 months ago #1303 by xavier
Replied by xavier on topic An error with rdd
Defining a larger rdd than default should fix your problem. You can do this by using the -rdd option to mdrun. We most often use a value of 1.4 or 1.5.

dujiangfeng wrote: Dear All,

I let my protein-membrane system run for a 10 micro seconds but it was a pity when the simulation at the time 273 ns, an error happened: "1 of the XXXX bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm)".
I think I understand this problem, and I also can find which atoms actually they are. But I don't know how to figure it out. I really appreciate if anyone can help.

Sjeng.

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

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