Vitaly Chaban wrote: > Hi Ran, > > I will try your advice. And for what purpose should '-mol' be used? > To cluster molecules. In this case, you topology is read from the .tpr file and all of the molecules there are taken into account for clustering. > 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 >
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