problem of simulating glucose molecule

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1

Dear lammps users,
I am facing a problem of simulating glucose molecule in lammps. Inside the data file of glucose, 24 atom types is showing but it actually should be 3 types due to the formula C6H12O6. If I use 24 atom types and put masses for all 24 atoms, it gives error “ERROR: Incorrect args for pair coefficients (…/pair_reaxc.cpp:288)”
But if I edited it to 3 atom types it showing error of “invalid atom types”. And I am using ffield.reax.cho force field.So please help me out.

Regards

Sasthi

2

You likely made a mistake when creating the data file.
Axel

3

Thank you Prof. Axel. I am using ovito to convert my pdb file into lammps data file. Are there any other option to make lammps data file from pdb file?

4

Please see https://lammps.sandia.gov/prepost.html

5

Also you probably will have to do the proper atom typing before the conversion.

And make sure you convert for atom style charge. There must be no bonds and other topology data included.
Axel

6

Thank you sir for the clarification. I got the error. The problem of defining the sequence of C6H12O6 was incorrect. After putting correct sequence as the masses are defined in file.data file, it is working fine. Thank you again sir. And one thing that as you said there should not be any bond and other topologies inside data file, so is it only for reax force field or for any other force field which are available in lammps, I have to make the data file in the format as you said?

7

What information may be in the data file is determined by the atom style, what information is required is determined by the force field. Some atom styles are supersets of others, so they are compatible, but may allow for information that can cause problems.

There is no simple rule and given the flexibility of lammps, it is only possible to reliably detect when information is missing, sometimes it can spot incorrect information, but never excess data for as long as it is compatible with the atom style.

It is the task user to feed lammps the proper information for the intended simulation. Never blindly trust any conversion tools. Especially if you convert from such a limited file format as pdb. Also make sure to convert to the suitable atom style. Some tools only support a few. Otherwise the GIGO principle applies.
Axel

8

Thank you sir for the clarification.