Hello,
I wish to compute rdf of Na+ ions around protein surface. I use the command:
g_rdf -f traj.xtc -n index.ndx -o rdf_prot_Na_res_com.xvg -b 40000 -s md.tpr
-surf mol -rdf res_com -bin 0.01
Since when -surf option is used, g_rdf does not normalize the rdf, I am
curious what does actually g_rdf reports in the output .xvg file? If we
refer to the Eq. (8.3) of gromacs_manual.pdf, which of the following value
gets reported in the output file:
1) \sum_{1,N_B} (\delta(r_{i,j}-r))
2) \sum_{1,N_B} (\delta(r_{i,j}-r)) / (4*pi*r^2)
3) \sum_{1,N_B} (\delta(r_{i,j}-r)) / (4*pi*r^2) / N_A
My hunch is that g_rdf -surf reports value calculated by Eq. 1 since
computing the term (4*pi*r^2) for an irregular surface is very complex.
Please advise ?
My second question is regarding the value of r_max. In the manual, it's
reported: Usually the value of rmax is half of the box length. When I
compute rdf using g_rdf -surf option, the value of maximum r is indeed half
the box length. However, I think the value of r_max, when -surf is used,
should be considerably less than the (box length)/2. If I am right, in this
case, r is the distance from the surface of the protein and not from the
center of the protein. Hence, r_max should be around the length of solvent
padding from protein surface.
Thanks,
Neeraj
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