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But I haven’t seen it!
You don’t see what?
Can the problem be in “dump” command where the information to be dumped is specified? how can I
What has the dump command got to do with it? A custom dump file doesn’t contain any information about bonding topology.
specify it in input file to replicate bonds and angles and dihedrals as well as atoms?
The replicate command works just fine. I repeat, if you want proof compute the energy of your system before and after the replication and compare the bonded energy contributions. Or if you want it in more detail, write a restart, convert it to a data file and look at that.
Axel
I mean I don’t see it in dump file. I’m trying to make my data file-a set of solvent molecules-using replicate command and a data file of a single molecule, which contains its coordinates, bonds, angles, and dihedrals. But what I only have after this is what is defined in dump file; atom id, mol id, and coordinates. This is only good for Atoms section in data file.
how can I have bonds, angles and dihedrals printed in dump file as well as atoms?
Reza
I mean I don’t see it in dump file. I’m trying to make my data file-a set of solvent molecules-using replicate command and a data file of a single molecule, which contains its coordinates, bonds, angles, and dihedrals. But what I only have after this is what is defined in dump file; atom id, mol id, and coordinates. This is only good for Atoms section in data file.
how can I have bonds, angles and dihedrals printed in dump file as well as atoms?
You cannot. Your approach is fundamentally flawed. As I mentioned before, the only way the write out the complete topology information is to write a restart.
A much better approach is to use a tool like packmol to generate initial configurations (just the coordinates) and then use a tool like the topotools plugin in VMD to establish the bonding information and what else (partial charges?) is needed for the potentials that you intend to use.
There are some examples for that on my homepage.
Axel