I am trying to use vnc viewer to take control of a computer in another location to simulate a protein using Gromacs 5.4.1. In the first step of simulation I am using GROMOS96 54a7 force field and the bellow command:
$ gmx pdb2gmx -f input.pdb -o output.gro water spce
but unfortunately I am getting this error:
[ERROR[ Illegal instruction (core dumped)
Kindly help me or suggest me to overcome/rectify the above error.
Hi Afsaneh,
Two things that come to my mind:
- do you actually start the command with the '$' sign in your terminal?
- in the remote computer, are you sure that gromacs is installed and compiled? In some cases, you have to first load a module, so that you can use an executable.
To check this you can simply type 'gmx' in the terminal, and see what it says.
Finally, make sure that input.pdb is in the path you are working at.
HTH.
Thank you so much dear Azade for your kind reply.
Yes, I do start the command with '$' sign. I have installed and compiled gromacs in the remote computer but I guess the problem might be related to the compiler and I am trying to fix it.
Try to use this command:
gmx pdb2gmx -f input.pdb -o output.gro water spce -ignh
Thank you so much dear Alireza,
Unfortunately this command does not work too. I am still getting the same error.
Look like your optimization dose not compatible with your hardware. Maybe you have to do reinstall Gromacs directly from the source of Gromacs. Look at the link bellow;
https://www.researchgate.net/post/How_do_you_fix_illegal_instruction_core_dumped_in_Gromacs_VERSION_465
Thank you very much dear Alireza and Azade for your generous advice. It is working well now.
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