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Software inconsistency error:Some interactions seem to be assigned multiple time
- cm
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4 years 11 months ago #8139
by cm
hi,
i am following the charmm gui martini maker system. My system consist of popc membrane bilayer, protein, water and ions.After system preparation charmm gui give two minimization.mdp and five equilibration.mdp. The minimization steps goes well but at the first equilibration step simulation has stopped with this error
Software inconsistency error: Some interactions seem to be assigned multiple time
even i have changed the minimization step from 5000 steps to 10000 steps, but still i am getting the same error.
Can anyone please suggest me how i can solve this.
thanking you
i am following the charmm gui martini maker system. My system consist of popc membrane bilayer, protein, water and ions.After system preparation charmm gui give two minimization.mdp and five equilibration.mdp. The minimization steps goes well but at the first equilibration step simulation has stopped with this error
Software inconsistency error: Some interactions seem to be assigned multiple time
even i have changed the minimization step from 5000 steps to 10000 steps, but still i am getting the same error.
Can anyone please suggest me how i can solve this.
thanking you
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- riccardo
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4 years 11 months ago #8140
by riccardo
Replied by riccardo on topic Software inconsistency error:Some interactions seem to be assigned multiple time
I think the system is blowing up (see
www.gromacs.org/Documentation/Errors#Sof...igned_multiple_times
).
I'm not so familiar with the charmm gui martini maker, but let's see.
Is the energy minimization converging? If not, you could try to increase further the energy minimization steps, and/or visually inspect your simulation box for bad overlaps (e.g., the protein coordinates overlapping strongly with some lipids, etc.)
I'm not so familiar with the charmm gui martini maker, but let's see.
Is the energy minimization converging? If not, you could try to increase further the energy minimization steps, and/or visually inspect your simulation box for bad overlaps (e.g., the protein coordinates overlapping strongly with some lipids, etc.)
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4 years 10 months ago #8142
by cm
Replied by cm on topic Software inconsistency error:Some interactions seem to be assigned multiple time
thank so much for your suggestion. i have tried so many things and after that i just get some hints from some previous similar problem that -rdd option can be used. my question is if i use -rdd 1.4 in production run, is there will be any problem to analyse results in future.
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4 years 10 months ago - 4 years 10 months ago #8143
by riccardo
Replied by riccardo on topic Software inconsistency error:Some interactions seem to be assigned multiple time
Increasing -rdd will not affect the physics of the simulation nor the analysis. It tells GROMACS to domain decompose your simulation box in larger suboxes when parallelizing. Indeed it might be required for some systems with Martini (see for example here
www.cgmartini.nl/index.php/tutorials/37-tutorial2
). I think -rdd 1.4 is fairly commonly used. Apparently, even larger -rdd may be needed with elastic networks (see again
www.cgmartini.nl/index.php/tutorials/37-tutorial2
). But mind that increasing -rdd lowers the performance of the simulations as you will decrease the amount of CPUs on which the simulation can run.
Last edit: 4 years 10 months ago by riccardo.
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