DvdS> But is your index a molecular index now? I think it should be in those DvdS> versions.
I tried both cases. The result is the same as in the present version. And the following comment is also present: "Using molecules rather than atoms. Not reading index file index.ndx" As for the error, it has magically disappeared after your email although the command line is the same as earlier... g_clustsize - mol -n index.ndx DvdS> Vitaly Chaban wrote: >> DvdS> Actually the text is incorrect (even the English is weird). If you use >> DvdS> the -mol flag the program will tell you that the index file is ignored. >> DvdS> If I recall correctly this wasn't always the case, and you could select >> DvdS> a subset of the molecules for this analysis. No clue why that >> disappeared. >> >> Yeah, without the possibility to select the groups to cluster there is >> no use of the '-mol' key in most cases because in the usual liquid the >> distances >> between particles are small enough and all the system appears to be >> one huge cluster... :) >> >> >> I just tried the same with gmx-3.3.1 but I broke with the following >> error: DvdS> But is your index a molecular index now? I think it should be in those DvdS> versions. >> >> Program g_clustsize, VERSION 3.3.1 >> Source code file: smalloc.c, line: 113 >> Fatal error: >> calloc for block->index (nelem=1069438469, elsize=4, file tpxio.c, line 906) >> ------------------------------------------------------- >> "Once Again Let Me Do This" (Urban Dance Squad) >> : Cannot allocate memory >> >> >> >> DvdS> Vitaly Chaban wrote: >>>> RF> In this case, you topology is read from the .tpr file and all of the >>>> molecules there are taken into account for clustering. >>>> >>>> >>>> I think you are right but the following text from the g_clustsize help >>>> message has confused me: >>>> >>>> >>>> " >>>> >>>> When the -mol option is given clusters will be made out of molecules rather >>>> >>>> than atoms, which allows clustering of large molecules. In this case an >>>> index >>>> >>>> file would still contain atom numbers or your calculcation will die with a >>>> >>>> SEGV. >>>> >>>> " >>>> >>>> >>>> So what is the sense to make index.ndx if ALL molecules are used for the >>>> calculation always... >> >> DvdS> Actually the text is incorrect (even the English is weird). If you use >> DvdS> the -mol flag the program will tell you that the index file is ignored. >> DvdS> If I recall correctly this wasn't always the case, and you could select >> DvdS> a subset of the molecules for this analysis. No clue why that >> disappeared. >> >>>> >>>> >>>> Vitaly >>>> >> _______________________________________________ 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
