Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupied by the metal atom and four dummy atoms in the 4 corners of square plane. I could successfully equilibrate my system and proceed with my simulation. While trying to make my 5-site model, a rigid body, I constrained a bunch of distances between atoms by using the option "constraints = all-bonds" option in the .mdp file and also defining a bunch of improper dihedrals in .itp file. It worked perfectly and later I wanted to shift to my 7-site model. So in my old 5-site model, I just added another 2 dummy atoms, one above and another below the square plane. I tried to make it rigid by constraining another bunch of distances, the same way as I did it before. However, I'm not able to perform energy minimization, during which I receive LINCS WARNING messages. Can you please suggest me, where am I going wrong ? I'm pasting below the atoms and bonds directive of .itp file.
[ atoms ] ; nr type resnr residu atom cgnr charge mass 1 M1 1 SET M 1 0.0 53.380 2 DZ1 1 SET D1 1 0.5 3.000 3 DZ2 1 SET D2 1 0.5 3.000 4 DZ3 1 SET D3 1 0.5 3.000 5 DZ4 1 SET D4 1 0.5 3.000 6 DZ5 1 SET D5 1 -0.5 3.000 7 DZ6 1 SET D6 1 0.5 3.000 [ bonds ] ; ai aj funct dist kb 1 2 1 0.06000 267520.0 1 3 1 0.06000 267520.0 1 4 1 0.06000 267520.0 1 5 1 0.06000 267520.0 2 3 1 0.08485 267520.0 3 4 1 0.08485 267520.0 4 5 1 0.08485 267520.0 2 5 1 0.08485 267520.0 1 6 1 0.02000 267520.0 1 7 1 0.02000 267520.0 2 6 1 0.06324 267520.0 3 6 1 0.06324 267520.0 4 6 1 0.06324 267520.0 2 7 1 0.06324 267520.0 3 7 1 0.06324 267520.0 thanks Debasmita _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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