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MARTINI 3 lipid bilayer simulation keeps crashing
- saini
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3 months 2 weeks ago #9717
by saini
MARTINI 3 lipid bilayer simulation keeps crashing was created by saini
Hi,
I am trying to simulate a lipid bilayer with chlorophyll molecules embedded. I am running an NPT equilibration; it runs for a few ns and then shows the below error.
Fatal error:
1 of the 54842 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (1.319 nm)
or the two-body cut-off distance (1.319 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck
Then, I used the -cpi and -append options to restart the simulation, then it started running. Again it stopped after a few ns showing the error. I am trying to complete the simulation run length by using the -cpi and -append options again and again.
Is there any solution to resolve this problem so that my simulation runs without crashing?
Help would be greatly appreciated!
Thank you!
I am trying to simulate a lipid bilayer with chlorophyll molecules embedded. I am running an NPT equilibration; it runs for a few ns and then shows the below error.
Fatal error:
1 of the 54842 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (1.319 nm)
or the two-body cut-off distance (1.319 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck
Then, I used the -cpi and -append options to restart the simulation, then it started running. Again it stopped after a few ns showing the error. I am trying to complete the simulation run length by using the -cpi and -append options again and again.
Is there any solution to resolve this problem so that my simulation runs without crashing?
Help would be greatly appreciated!
Thank you!
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