Dear experts,
I am trying to perform a production run of several proteins in a water environment according to several tutorials. After the production, one of the analysis I am interested in is the evaluation of a radial distribution function around each bead of the chain.
I am trying with the module gmx rdf but I am havint some trouble in specifying that the calculation should be done for a specific segment and not the center of mass of the entire chain. Do you have any suggestion?
Thanks in advance.
1. You may create an index file to compute the RDF for the desired groups.
2. In VMD, the RDF can be calculated using the GUI under Extensions > Analysis > Radial Pair Distribution Function g(r). You can specify atom selections directly in the GUI, and an index file is not required.
1. Create an index file with the specific segment as a separate group. You can use the make_ndx command for this. If you want to create a group for residues 1 to 20:
$echo -e "r 1-20\nq" | gmx make_ndx -f md.gro -o index.ndx
This command will create a new group with residues 1 to 10 and save the index file as index.ndx.
2. Calculate the RDF using the gmx rdf command and specify the new group as one of the groups for which to calculate the RDF:
$echo -e "Group1\nGroup2" | gmx rdf -s md.tpr -f md.xtc -n index.ndx -o rdf.xvg