Hallo!
I try to create a simple model for a simulation of DNA-packing. For the
first step, I create atoms, which have the same size and same
characters. Now I try to create some bonds between this atoms. I know,
that I have to define the bonds in a data-file. So my problem is, that
lammps ignores these bonds. For this beads-on-a-string model it is
necessary that there are so many as possible chemical information or
cutoffs in it. Is there a possibility to turn this off? The bonds (it
should be only 1 bond-type) it has to be that one atom has a maximum of
two neighbors like: 1-2 2-3 3-4 4-5...
I write my data script like this:
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 1 10 11
11 1 11 12
12 1 12 13
13 1 13 14
14 1 14 15
15 1 15 16
16 1 16 17
Maybe one of you could help me. Thank you
Best regards Ulrike
hallo ulrike,
Hallo!
I try to create a simple model for a simulation of DNA-packing. For the
first step, I create atoms, which have the same size and same
characters. Now I try to create some bonds between this atoms. I know,
that I have to define the bonds in a data-file. So my problem is, that
lammps ignores these bonds. For this beads-on-a-string model it is
how do you know? did you check the bonded energy output?
necessary that there are so many as possible chemical information or
cutoffs in it. Is there a possibility to turn this off? The bonds (it
should be only 1 bond-type) it has to be that one atom has a maximum of
two neighbors like: 1-2 2-3 3-4 4-5...
I write my data script like this:
please check out:
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1
for an example of conveniently setting up custom bead spring
models with VMD scripting. the data file writer has been thoroughly
tested, so you can be assured that its output format will be correct.
however, whether lammps actually applies bonded forces and how
strongly depends on your bond_coeff parameters.
cheers,
axel.