You can calculate properties describing molecular shape using PLUMED as a trajectory post-processing tool. Example input:
GROUP ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47 LABEL=al GYRATION TYPE=RADIUS ATOMS=al LABEL=rg_al GYRATION TYPE=TRACE ATOMS=al LABEL=tr_al GYRATION TYPE=GTPC_1 ATOMS=al LABEL=gtpc1_al GYRATION TYPE=GTPC_2 ATOMS=al LABEL=gtpc2_al GYRATION TYPE=GTPC_3 ATOMS=al LABEL=gtpc3_al GYRATION TYPE=ASPHERICITY ATOMS=al LABEL=asph_al GYRATION TYPE=ACYLINDRICITY ATOMS=al LABEL=acyl_al GYRATION TYPE=KAPPA2 ATOMS=al LABEL=K2_al GYRATION TYPE=RGYR_3 ATOMS=al LABEL=g3_al GYRATION TYPE=RGYR_2 ATOMS=al LABEL=g2_al GYRATION TYPE=RGYR_1 ATOMS=al LABEL=g1_al PRINT ARG=rg_al,tr_al,gtpc1_al,gtpc2_al,gtpc3_al,asph_al,acyl_al,K2_al,g3_al ,g2_al,g1_al STRIDE=1 FILE=shape_hsp90 -- ====================================================================== Dr Thomas Evangelidis Post-doctoral Researcher CEITEC - Central European Institute of Technology Masaryk University Kamenice 5/A35/2S049, 62500 Brno, Czech Republic email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.