I want to calculate the COM RDFs between my peptide and water for which I have used the -com option in gromacs.(Also tried with -com and -rdf res_com).
It generates a wierd RDF which does not look correct. I want to take the first minimum and use the -cn option to get the coordination number.
The images for the RDFs are attached herein. What could be possibly wrong? The atom-atom RDFs are coming out well but not the COM ones.
Additionally,
If I use the -cn option of gromacs, it shows the cumulative CN right? Which means if I see the number at 0.257(say that's the cut-off), the number corresponding to it would be the coordination number. Am I right?
What if I integrate the rdf using g_analyse -integrate option ?
Any ideas on how to do the integration in Gromacs?
making an index file and showing it in calculation of RDF is much easiest way to do it. indicating whole protein while you are creating an index file leads to take COM automatically in RDF calculations.
- Badges
- Science topic
- Similar topics
- Applied Mathematics
- Calculations