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Error during self-assembly
- Bharath
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11 years 6 months ago - 11 years 6 months ago #1170
by Bharath
Error during self-assembly was created by Bharath
While attempting the tutorial, I made a box of size 7.5 x 7.5 x 7.5 nm^3, filled with 128 DSPC lipids. After repeated energy minimization steps using the em.mdp file (until convergence was achieved), I added 768 molecules of water, as specified. I then minimized the structure once again, and then attempted the bilayer self assembly using md.mdp.
However, I obtained the following error after about 100000 steps of the simulation:
"1 of the 2966 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), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck"
The same error was avoided if I increased the box size to 10x10x10 nm^3, and removed the maxsol criterion. However, this left me with a disproportionately large number of water molecules. I have come across the term 'blowing up' in MD simulations, but being new to GROMACS, I'm not completely sure how to counter such an error.
Could you please help me with this? Thanks a lot!
However, I obtained the following error after about 100000 steps of the simulation:
"1 of the 2966 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), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck"
The same error was avoided if I increased the box size to 10x10x10 nm^3, and removed the maxsol criterion. However, this left me with a disproportionately large number of water molecules. I have come across the term 'blowing up' in MD simulations, but being new to GROMACS, I'm not completely sure how to counter such an error.
Could you please help me with this? Thanks a lot!
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- djurre
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11 years 6 months ago #1174
by djurre
Replied by djurre on topic Error during self-assembly
It's a bit too vague to give an very exact answer. You might try to set the the flag '-rdd 1.6' for mdrun. But normally that should not be necessary for lipid simulations. So the problem might come back in some other way.
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- Yufeng
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11 years 5 months ago #1213
by Yufeng
Replied by Yufeng on topic Error during self-assembly
I obtained the same error at the same step.:P.Then i set the flag -rdd as you said,it successed.I notice that some people enconunted the error during the simulation,others are not.it's odd somehow.anyway,thanks for your suggestion.
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