[email protected] 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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
