Hi everyone, I hope you're all safe and doing great.
So I cannot install my Gromacs in my laptop, so I used SLURM HPC instead for MD. The Gromacs input files that I used were generated in CHARMM-GUI Polymer Builder. I was surprised to see that in the previous files I've generated, there was suddenly an "index.ndx" file, which was not in my previous input files.
I followed the "README" file but, the MD run stopped at minimization and I saw this in the .err file: "Fatal error: Group SOLV referenced in the .mdp file was not found in the index file."
I read a similar thread to this and the researcher was told to put "gmx make_ndx -f em.gro -o index.ndx". I did the same thing but I still got an error saying that the "em.gro" file cannot be found.
Another question, I did not change the way I generate input files, do I have to repeat the input files I've generated earlier that did not have an "index.ndx" file in them?
Please help me out, thank you so much!
(Attached are relevant files)
It would also be helpful to attach your MDP file here. In your job script, you are creating the index group after running minimization. If a new group is defined in mdp file (solv in your case), that also needs to be defined in that way using make_ndx command before compiling all the inputs. Default groups generated by gromacs contain SOL group for solvent.. if that's the group you're referring to in your mdp, rename it in mdp..
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