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Self-assembly of functionalized alkanes on a graphite surface
- Daisuke
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3 years 8 months ago #8658
by Daisuke
Self-assembly of functionalized alkanes on a graphite surface was created by Daisuke
I am running the MD simulation of the tutorial for Self-assembly of functionalized alkanes on a graphite surface using GROMACS 2020.
At the stage of 2. Equilibration, I have the error massage as below:
"gmx(59696,0x7fffbd2ca3c0) malloc: *** error for object 0x7fce5dc092b8: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6"
Thanks a lot in advance for anyone who can help me with these!
At the stage of 2. Equilibration, I have the error massage as below:
"gmx(59696,0x7fffbd2ca3c0) malloc: *** error for object 0x7fce5dc092b8: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6"
Thanks a lot in advance for anyone who can help me with these!
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- bart
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3 years 8 months ago #8659
by bart
Replied by bart on topic Self-assembly of functionalized alkanes on a graphite surface
This sounds like a GROMACS error, I would try their mailinglist, they usually respond fast and in a helpful manner.
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- vainikka
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3 years 8 months ago #8660
by vainikka
Replied by vainikka on topic Self-assembly of functionalized alkanes on a graphite surface
Hey.
This is way outside my area of expertise, so take this with a grain of salt.
I think there are two possibilities for your error: Either your system runs out of memory, or GROMACS has a bug. You can install an earlier version of GROMACS (for example 2019.6) and try running the same simulation with that. If you still get the same errors, it's likely due to issues with your local machine.
You should also post the GROMACS related questions on the GMX forums, you'll get more detailed answers there.
This is way outside my area of expertise, so take this with a grain of salt.
I think there are two possibilities for your error: Either your system runs out of memory, or GROMACS has a bug. You can install an earlier version of GROMACS (for example 2019.6) and try running the same simulation with that. If you still get the same errors, it's likely due to issues with your local machine.
You should also post the GROMACS related questions on the GMX forums, you'll get more detailed answers there.
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- Daisuke
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3 years 8 months ago #8661
by Daisuke
Replied by Daisuke on topic Self-assembly of functionalized alkanes on a graphite surface
Thank you very much!
I'll try to ask the question on the GROMACS forum.
I'll try to ask the question on the GROMACS forum.
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3 years 8 months ago #8662
by Daisuke
Replied by Daisuke on topic Self-assembly of functionalized alkanes on a graphite surface
Thank you very much!
I'll try it again by using the GROMACS 2019.
I'll try it again by using the GROMACS 2019.
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