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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-CA link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hello,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for your attention. A word was missing in my previous e-mail!! The g(r) is NOT normalized.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Here was my command:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>g_rdf -f traj.xtc -s topol.tpr -n reidues_atoms.ndx -o gofr -surf res<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The index file includes atoms in the side chain exposed to the solvent:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>[ SideChain_&_r_13_r_17_r_19-21_r_24 ]<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 144 145 146 147 148 149 150 151 152 189 190 191 192 193 194<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 195 196 197 198 221 222 223 224 225 226 227 228 229 230 231<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 247 248 249 250 285 286 287 288 289 290 291 292 293 294 295<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 296 297 298<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Sorry for inconveniences in the first iteration.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>paymon<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Mark Abraham<br><b>Sent:</b> February-13-12 12:06 AM<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> Re: [gmx-users] g_rdf -surf<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>On 13/02/2012 5:54 PM, Payman Pirzadeh wrote: <o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hello,</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>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.</span><o:p></o:p></p><p class=MsoNormal><br>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.<br><br><br><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>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?</span><o:p></o:p></p><p class=MsoNormal><br>If it's already normalized, what do you want to do? 41000 is what quantity?<br><br>Mark<o:p></o:p></p></div></body></html>