read data

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1

Dear Users,

I am trying to use an input of .pdb format file as my input file (for coordinate) .In the manual the command options to be used in the lammps input file suggests the use of read data option , what other file can we use and as mentioned in the documentation, restart file specify the use of lammps restrt file only .
How can I work out if I having a .pdb file made in DS viewer Pro.

Thank
John

2

You can only use a data file in the documented format. You can use VMD
and the topotools plugin to create a data file based on the
coordinates in the pdb file.

Axel

3

After defining the input file in VMD using topotools plugin , I use to read this file in my lammps input file as read data.
This gives me an error on pair coefficient.

(All pair coefficients are not set).

Thanks
John

4

After defining the input file in VMD using topotools plugin , I use to read
this file in my lammps input file as read data.
This gives me an error on pair coefficient.

(All pair coefficients are not set).

sure. topotools is no magician. so how should
it know your force field parameters?

a pdb file certainly doesn't contain that information.

axel.

5

I am trying to use this for a polymer in box , I only have four atom types in my input file in a 10 mer polymer chain with different residue numbers in my .pdb file .
I tried this with pair_coeff * * 1.0

Do I need to specify for each atom in my read data file.

Thank You
John

6

I am trying to use this for a polymer in box , I only have four atom types
in my input file in a 10 mer polymer chain with different residue numbers in
my .pdb file .
I tried this with pair_coeff * * 1.0

Do I need to specify for each atom in my read data file.

i don't understand the question. are you saying that
you want to do an MD simulation and that you
have absolutely no idea of what interaction you have
to assign to what?

am i correct to assume that you have never done MD
before and never looked into a text book on MD?

axel.