Hi, Use -n without -mol. Clustering will be atom based. Good luck, Ran.
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 > > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman ------------------------------------------------------ _______________________________________________ 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