normal segmentation fault with mdrun

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13 years 7 months ago #392 by braunar
segmentation fault with mdrun was created by braunar
I am new to using martini. I am trying to execute the lipid self-assembly tutorial using gromacs v4.0.7 however I get to the first mdrun step and get a segmentation fault.

This is the output I get:
mdrun -v -c 128 minimised.gro

Getting Loaded...
Reading file topol.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 500
Step= 0, Dmax= 1.0e-02 nm, Epot= 5.89692e+06 Fmax= 1.41449e+07, atom= 1555
Segmentation fault

There were no warnings at the grompp step and I am perplexed about this problem.
Any help would be greatly appreciated.
Anthony

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13 years 7 months ago #395 by xavier
Replied by xavier on topic segmentation fault with mdrun
mdrun -v -c 128 minimised.gro

This command line does not make much sense! The 128 seems to be not necessary!

XAvier.

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13 years 7 months ago #407 by wenchangyu2006
Replied by wenchangyu2006 on topic segmentation fault with mdrun

xavier wrote: mdrun -v -c 128 minimised.gro

This command line does not make much sense! The 128 seems to be not necessary!

XAvier.


Actually I also tried the tutorial and when I arrived here I use command "mdrun -v -c minimised.gro ", which is exactly the same as the command in the tutorial. But I still got the same error message. Has anybody went through that tutorial? Thanks a lot.

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13 years 6 months ago #410 by xavier
Replied by xavier on topic segmentation fault with mdrun
Yes people have been using this tutorial successfully.

The minimization may have not been through correctly.

Please check it and report back.

XAvier.

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13 years 6 months ago #413 by wenchangyu2006
Replied by wenchangyu2006 on topic segmentation fault with mdrun
you mean I have to do the minimization with more steps, maybe also with constraints released gradually? Could you give more information about the minimization problem? Thanks a lot.

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13 years 6 months ago #414 by xavier
Replied by xavier on topic segmentation fault with mdrun
Well more steps or change the starting structure ... but make sure that your minimized structure does not have any problem ... check the max force and the potential energy value ...

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