I am currently going through the following tutorial for replica exchange MD on gromacs: https://www.gromacs.org/@api/deki/files/209/=tutorial.pdf
When I got to stage 2 and tried to create the .tpr files using the command,
(for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t equil-state; cd ..; done)
I get this error:
Program: gmx grompp, version 2018.2
Source file: src/gromacs/fileio/checkpoint.cpp (line 531)
Function: int doVectorLow(XDR*, StatePart, int, int, int, int*, T**, std::vector*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; XDR = XDR; FILE = _IO_FILE]
Assertion failed:
Condition: list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr)
Without list, we should have exactly one of v and vector != NULL
I have no idea why this error is occurring, as I'm following the tutorial almost exactly. From searching online, it seems like other people have came across a similar problem, although I can't find any solutions.
Any help would be appreciated!
Dear Bibo Feng
Have you tried running the commands one by one by hand and see if the problems is GROMACS related or loop/bash related?
Just cd into equil0, run the grompp command and check the output.
Best,
Nicola
Bibo Feng , can you share how have you solved the problem?
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