Dear scholars,
Does any one know what will be the steps if I want to run MD of organic ligand in water using gromacs? I successfully ran the "Lysozyme in Water" tutorial from Gromacs Tutorial site but, here I want to replace lysozyme with organic ligand. I tried to follow same tutorial but I got error in the nvt equilibration that is attached here. I want to investigate the conformational flexibility of ligand. I need your kind suggestions. Thank you
Sincerely,
Shravan
Hello Shravan B Rathod,
The cause of this issue is that the filesystem might not be able to handle files >2GB. So u need to decrease output to the file so that the filesize is
Dear Mehrdad Mohebi,
Thanks so much for your quick response. I'll check that.
you're welcome
If my answer was useful, recommend it.
Best wishes
Hi Shravan,
the error seems clear in stating that the mdp file for the NVT equilibration step you used from the lysozyme tutorial still retains the protein term in the tc_groups section. Since your system contains only the solvent and organic ligand and not a protein macromolecule, you need to delete the protein term and only retain the non-protein term in the NVT mdp files. You need to alter these parameter files based on your system and force field used.
Hey Aditya. i have tried that like this
tc-grps = Non-Protein Non-Protein
but got the same error. Please help and thanks in advance.
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