I am performing the EM steps (Gromacs Version 2021.1) but whenever I do so, I am getting Segmentation Fault (Core Dumped) Error. I have also even tried to reduce the parameter
emtol = 100.0 ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep = 0.02 ; Minimization step size
nsteps = 200 ; Maximum number of (minimization) steps to perform
But still, I am getting the same error for the past few days.
I will be very thankful if anybody can help in sorting this error.
Below, I am attaching the screenshot of the error file (.jpg), em.log.1 file, and topology file of mine molecule.
Thanking You.
Hey,
Most of the time, the segmentation error occurs when the machine does not have the required amount of allocated memory. Try to do it with a smaller simulation system (number of atoms)
Hello Stéphane Abel, I have performed all steps on Ubuntu through Windows 10 Partition.
Stéphane Abel I have installed the Gromacs 2021.1 in the same manner as mentioned on their installation site (attached jpg image below). My system is of Intel I3 8th generation provided with 8gb Ram.
Stéphane Abel Thank you so much for providing your valuable time. I'm sorry earlier I couldn't get your question based on the size of the system.
The answer is
1. complex_box.gro = 12938 atoms
2. complex_ions.gro = 20506518 atoms
3. complex_solvated.gro = 20506532 atoms
I have also inboxed you the visualization pdf file for the same.
Thanks a lot.
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