Hi Ran, I will try your advice. And for what purpose should '-mol' be used?
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
