Dear All I am creating a truncated octahedron box and in vmd it appears as a rectangular box. In mailing list it has been suggested to use trjconv -ur compact option. But I have two issues,
1) I get box vector angle 70 90 70 with editconf and should be around 109 109 109 for a truncated octahedron box editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron system size : 12.324 14.348 5.952 (nm) diameter : 15.385 (nm) center : 7.774 7.569 7.829 (nm) box vectors : 12.324 14.348 5.952 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume :1052.41 (nm^3) shift : 1.119 5.007 -0.568 (nm) new center : 8.893 12.576 7.261 (nm) new box vectors : 17.785 17.785 17.785 (nm) new box angles : 70.53 109.47 70.53 (degrees) new box volume :4330.63 (nm^3) 2) I have a same system in AMBER and using truncated oct box with same 12 Angstrom water buffer but in Gromacs I get almost twice water molecules as I get in AMBER but with AMBER I get 109 109 109 vector angles. Just to add in AMBER I used the default value of closeness of solvent molecules being 1.0 Angs. I am not sure whats default in editconf (though I see it uses default water density value) Please suggest why I am getting different vector angles and number of waters? best regards JIom -- 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.