Queries regarding read_data command for simulating multiple systems in a single simulation

Hello everyone,

I am trying to run a simulation which contains protein system and a carbohydrate system. Both the data files are created using CHARMM forcefield. I have used the syntax:

read_data quad.data extra/atom/types 100 extra/bond/types 100 extra/angle/types 100 extra/dihedral/types 100 extra/improper/types 100 extra/dihedral/per/atom 25
read_data Hyal.data add append offset 23 48 120 236 16

The two systems have non-bonded interaction between them.

But it's giving an error "Not all pair coefficients are set".

According to the example given in the documentation page, I need to set the pair-wise interaction coefficients for the interaction between the atoms in the two data files.

The number of atom types one data file is 23 and the other is 16.

Does it mean I have to set all pair coefficients for 23 types of atoms interacting with 16?

Or is there any other way to get around this which will work the same way as merging the data files into a single one?

Hi

Have you tried to use the pair_modify command with the “appropriate” mix value? This should take care of the interactions between the unlike atom types.
It might be useful to have a look at the “How to” section 6.3 where there is a description how to implement CHARMM in LAMMPS.

Hope it helps !
Evangelos

Στις Τετ, 1 Μαΐ 2019 στις 9:16 π.μ., ο/η Shambo Bhattacharya via lammps-users <[email protected]> έγραψε:

Hi,

Yes. Pair_modify has been used initially at the start of the simulation. All the initiating input as shown in How to section has also been implemented.

Hello everyone,

I am trying to run a simulation which contains protein system and a
carbohydrate system. Both the data files are created using CHARMM
forcefield. I have used the syntax:

read_data quad.data extra/atom/types 100 extra/bond/types 100
extra/angle/types 100 extra/dihedral/types 100 extra/improper/types 100
extra/dihedral/per/atom 25
read_data Hyal.data add append offset 23 48 120 236 16

The two systems have non-bonded interaction between them.

But it’s giving an error “Not all pair coefficients are set”.

in your read_data command you request 100 extra atom types. you have to set pair_coeff for all of them. same for bond, angle, dihedral and improper. you must set them, even if you don’t use them.

According to the example given in the documentation page, I need to set
the pair-wise interaction coefficients for the interaction between the
atoms in the two data files.

when trying to read multiple data files, it is best to not have any Coeff sections in the data file, but set those explicitly with pair_coeff and bond_coeff and so on in the input.

The number of atom types one data file is 23 and the other is 16.

so why are you then requesting 100 extra atom types and not only 16?

Does it mean I have to set all pair coefficients for 23 types of atoms
interacting with 16?

Or is there any other way to get around this which will work the same
way as merging the data files into a single one?

if you are starting with CHARMM data (.psf .crd/.pdb) it is probably easier to merge those two systems first and then you need only one read_data command.

axel.