Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows: g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac avclust.xvg -mc maxclust.xvg I have 150 monomer initially in my system. I selected -cut from rdf.xvg for tail-tail that 0.7 was the first minimum in this graph.
1- the nclust.xvg file is as follows: @ title "Number of clusters" @ xaxis label "Time (us)" @ yaxis label "N" @TYPE xy 0.000000e+00 104 6.000000e+01 88 1.200000e+02 89 1.800000e+02 85 2.400000e+02 79 3.000000e+02 79 3.600000e+02 91 4.200000e+02 89 . . . . . .. . .. . .. . .. ... . . . ... . .. .. .. . . .. . .. .. . . ... . . . . ... ............. whereas in the first step of simulation there is no cluster and it should be 0!!! 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them about time either file .xvg and graphs!!!why and where is problem? 3- how should I find the number of monomers from first to end of simulation that it should be 150 in the first step. May I ask you to help me, Please? Thank you in advance. Best Regards Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
