I did a MD simulation in gromacs for a protein and I would like to calculate the RMSD just for a part of the protein instead that for the whole protein. Any idea how to do that?
All you need to do is run gmx make_ndx on any coordinate or .tpr file and select the region of interest (type "help" for examples, the syntax is quite simple). Then you pass the index file to gmx rms -n and choose the group for output. You don't need to run the simulation again, you just have to analyze it properly (note that much of this is discussed in the GROMACS manual, either the PDF or online at manual.gromacs.org)
Justin, thank you very much for the answer. I haven't done that before. Could you please share an example of the command line? do I need to run again the simulation or just generate the rmsd file?
All you need to do is run gmx make_ndx on any coordinate or .tpr file and select the region of interest (type "help" for examples, the syntax is quite simple). Then you pass the index file to gmx rms -n and choose the group for output. You don't need to run the simulation again, you just have to analyze it properly (note that much of this is discussed in the GROMACS manual, either the PDF or online at manual.gromacs.org)
There is no such function in VMD program? That can calculate the RMSD for selected residues?
Thanks
Hello Justin
Your explanation was indeed informative but i am confused that which groups i need to choose when i want to calculate C-alpha RMSD of a protein???
Group for LSF = Protein/Calpha
Output Group = Protein/ Calpha
or LSF/Output= Calpha/Calpha
or LSF/Output = Pro/Pro
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