Hello, Thanks for your attention. A word was missing in my previous e-mail!! The g(r) is NOT normalized.
Here was my command: g_rdf -f traj.xtc -s topol.tpr -n reidues_atoms.ndx -o gofr -surf res The index file includes atoms in the side chain exposed to the solvent: [ SideChain_&_r_13_r_17_r_19-21_r_24 ] 144 145 146 147 148 149 150 151 152 189 190 191 192 193 194 195 196 197 198 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 285 286 287 288 289 290 291 292 293 294 295 296 297 298 So, I am trying to calculate the RDF of water molecules (SOL) with respect to the surface of the residues whose side chain atoms are listed in the index file. What I get is a small peak in the order of 0.05 the beginning, and then, g(r) is increasing to 41000. Sorry for inconveniences in the first iteration. Best, paymon From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: February-13-12 12:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf -surf On 13/02/2012 5:54 PM, Payman Pirzadeh wrote: Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. Please supply the actual command line copied and pasted, as well as which groups you specified and what they contain. The information above is confusing. However, the calculated RDF rises up to 41000 in long distances. It appears that it is normalized (as specified by the help). How can I normalize this function? If it's already normalized, what do you want to do? 41000 is what quantity? Mark
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