To my knowledge, g_rdf calculate all the atoms of group A to all the atoms of group B to get the gAB(r). g_rdf -com calculate the center of group A, not the centers of the residues in group A to all the atoms of group B.
I upload a file based on gmx_rdf.c to calculate the centers of residues of group A (and B) last month to the website of gromacs. 2006/11/22, Nguyen Hoang Phuong <[EMAIL PROTECTED]>:
My question is that how does gromacs compute g(r)? Is r the distance between center of mass of the group [ Pep ] and the center of mass of each solvent molecule? Or gromacs computes g_i(r) between each atom of the group [ Pep] with respect to solvent molecules and then take average over all g_i(r) to get g(r)? Many thanks in advance, Phuong _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Baofu Qiao
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