[gmx-users] regarding rmsd calculation of protein

[SHAHEE ISLAM]

hi,
i have two protein in my gro file.when i am calculating rmsd by this command
g_rms -s dynamic.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
 this options are coming
Group     0 (         System) has 12059 elements
Group     1 (        Protein) has   566 elements
Group     2 (      Protein-H) has   566 elements
Group     3 (        C-alpha) has     0 elements
Group     4 (       Backbone) has     0 elements
Group     5 (      MainChain) has     0 elements
Group     6 (   MainChain+Cb) has     0 elements
Group     7 (    MainChain+H) has     0 elements
Group     8 (      SideChain) has   566 elements
Group     9 (    SideChain-H) has   566 elements
Group    10 (    Prot-Masses) has   566 elements
Group    11 (    non-Protein) has 11493 elements
Group    12 (          Other) has 11493 elements
Group    13 (              W) has 11477 elements
Group    14 (            ION) has    16 elements
for this reason i am able to calculate the rmsd of two protein
together by selecting 1.
but i want to calculate the rmsd of the protein individualy.how i will do this.
My .gro file consist of atom no 1 to 283 for protein1 and atom no 284
to 566 for protein2.
thanking you
shahee islam
university of calcutta