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: 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 >> =============================== 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
