Hi Ran, Then for what purpose should '-mol' be used?
In my case it's more convenient to have molecule-based clustering rather than atom-based (in histo-clust.xvg, nclust.xvg, etc). Looking only at the number of atoms in the cluster it is sometimes very difficult to determine how many molecules of different types are there. Especially when there are many clusters and several types of molecules (ions). Thanks, Vitaly RF> Hi, RF> Use -n without -mol. Clustering will be atom based. RF> Good luck, RF> Ran. RF> Vitaly Chaban wrote: >> Hi GMX Colleagues, >> >> I need a little clarification. >> >> I try to calculate a distribution of clusters of ions in a system with >> several cations and anions and a few solvent molecules. So I just need >> a number of cluster consisting of ions and the size of the each (how many >> ions the cluster includes). >> >> To do this I use >> g_clustsize(402) -n index.ndx -mol -s topol.tpr >> where index.ndx contains only the number of the atoms of the ions. >> >> but the programme outputs: >> Back Off! I just backed up temp.xvg to ./#temp.xvg.1# >> Reading frame 0 time 0.000 Reading file topol.tpr, VERSION 4.0.2 >> (single precision) >> Reading file topol.tpr, VERSION 4.0.2 (single precision) >> Using molecules rather than atoms. Not reading index file index.ndx >> >> Why does it not read the index file with the atom number I want to >> cluster? >> >> >> When I see for example histo-clust.xvg: >> >> @ title "Cluster size distribution" >> @ xaxis label "Cluster size" >> @ yaxis label "()" >> @TYPE xy >> 0 0.000 >> 1 19.531 >> 2 4.583 >> 3 1.707 >> 4 0.647 >> 5 0.259 >> 6 0.060 >> 7 0.140 >> 8 0.048 >> 9 0.054 >> 10 0.020 >> 11 0.022 >> 12 0.000 >> ................ >> ................ >> ................ >> 577 31.096 >> 578 33.457 >> 579 36.982 >> 580 28.942 >> 581 31.311 >> 582 34.850 >> 583 38.401 >> 584 30.307 >> >> >> It looks like all the atoms in the system were used to find clusters. >> >> And maxclust.xvg: >> >> @ title "Max cluster size" >> @ xaxis label "Time (ps)" >> @ yaxis label "#molecules" >> @TYPE xy >> 0.000000e+00 577 >> 1.000000e-01 576 >> 2.000000e-01 565 >> 3.000000e-01 550 >> 4.000000e-01 567 >> 5.000000e-01 572 >> 6.000000e-01 566 >> 7.000000e-01 578 >> 8.000000e-01 567 >> 9.000000e-01 565 >> 1.000000e+00 563 >> 1.100000e+00 579 >> 1.200000e+00 566 >> >> >> >> Please anybody let me know how to find clusters only among those >> particles I point out in the index file. So I need only the clusters >> consisting of ions but solvent is not of interest in my case. >> >> >> Thank you in advance, >> Vitaly >> >> >> >> =============================== >> Vitaly V. Chaban, Ph.D.(ABD) >> School of Chemistry >> V.N. Karazin Kharkiv National University >> Svoboda sq.,4, Kharkiv 61077, Ukraine >> email: cha...@univer.kharkov.ua,vvcha...@gmail.com >> skype: vvchaban, mob.: +38-097-8259698 >> _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
