I am running the MARTNI coarse grain simulation of the tutorial for Self-assembly of functionalized alkanes on a graphite surface established for GROMACS 5 and higher.
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!
The error message only points to some memory allocation that went wrong. In itself, the message is too vague to give you specific advice, what I can say is that this usually only happens when GROMACS is doing something off bounds - not maybe not reading a Martini force-field parameter properly or starting a simulation with two atoms on top of one another which will lead to enormous forces, and has been greatly reduced in later versions of the software.
A first thing to check is, if you are using the GROMACS version that matches the tutorial material. Usually GROMACS tries to maintain a stable interface throughout versions, but especially in combination with external inputs from MARTINI there might be some unintended mismatches.
Thank you for the information.
I am happy to understand the cause. Tomorrow we will install GROMACS version 16.6 which matches the MARTNI tutorial.
It’s so kind of you!