Error when following the tutorial in Gromacs, example 1 #76
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I was following the tutorial of SIRAH in Gromacs: This restraint.gro file was not mentioned before this step. What's going on? |
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Replies: 2 comments
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The tutorial used a old version of GROMACS. If you use GROMACS 2018 or even newer version, "-r" flag should be typed explicitly in the "gmx grompp" command. Further details of how to use 'gmx grompp' in GROMACS 2018 including the '-c' and '-r' flags can be found here: Let us know if it works. |
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Thanks! Since it's 2024 now, I doubt any user would use a version of Gromacs older than the 2018 version. it's better to modify the tutorial. You can close this ticket after doing so. |
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The tutorial used a old version of GROMACS. If you use GROMACS 2018 or even newer version, "-r" flag should be typed explicitly in the "gmx grompp" command.
Thus, you just need to repeat the same .gro file as the -c flag, as the error message explains.
Something like:
gmx grompp -f ../sirah.ff/tutorial/1/GPU/eq_CGDNA.mdp -p ../topol.top -po eq.mdp -n ../dna_cg_ion.ndx -c dna_cg_em.gro -r dna_cg_em.gro -o dna_cg_eq.tpr
Further details of how to use 'gmx grompp' in GROMACS 2018 including the '-c' and '-r' flags can be found here:
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-grompp.html
Let us know if it works.