Hi Mark, Initially I included all the sets of bonds (as you have mentioned). Then I get the warning message while doing grompp, which says number of constraints is more (18 as I've defined) than required (it shouldn't be more than 15). With all the sets of bonds defined also, energy minimization didn't happen. Later I excluded 5-6, 4-7 and 5-7 from the list. However, nothing works.
thanks > dbis...@ucalgary.ca wrote: >> 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 > > If the symmetry of the system is to be octahedral, then you should try > defining a symmetric set of bonds. You've omitted 5-6, 4-7 and 5-7. > > Mark > _______________________________________________ > 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 > > > _______________________________________________ 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
