I have a problem in generating data file which I’d appreciate it if you help me to solve it. For preparing a simulation I need a to move a molecule to a specific location and equilibrating the system and then generating a new data file for further simulations. I have tried different scenarios to make the data file but all failed except one. By the way I’m using lammps-icms which I pulled March 20.
Below are the styles that are used in my input file:
Here is the list of my trials:
I ran the simulation for designated time steps and after that I used :
This gives me a data file but the problem is that it writes some negative types in the Dihedrals section which makes the data file not to be usable. I was wondering where those negative types are coming from?
dump dcd :
I dumped a dcd file at the desired time step and then I used dcd and psf file to open it in vmd generate a data file in vmd by using topo writelammpsdata command. This gives me a data file with incorrect number of bonds, angles, dihedrals types and the first few lines of it is as below:
LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.2 on Wed May 21 13:33:07 CDT 2014
11 atom types
1 bond types
1 angle types
1 dihedral types
1 improper types
-25.467230 24.532770 xlo xhi
-24.936508 25.063492 ylo yhi
-48.315960 48.084209 zlo zhi
What’s the problem? Isn’t a dcd loaded with psf enough for generating data file with topotools.
- I read dcd and psf file in vmd and I saved a pdb from the desired frame. I used charmm2lammps tool to generate a data file using the psf, charmm parameter file, charmm topoloy file and the generated pdb file. This one gives me a clean working data file.
I appreciate your help.