How to generate Lammps input script for Coarse Grained Polymer?

LAMMPS LAMMPS Beginners
1

Dear All,

Actually, I am currently working on coarse graining of polymer, then I want to simulate, I am stuck in which that how doing coarse graining.

#filename:"test.in", this is an example input file
units lj #use reduced units
atomstyle angle #set potential style
readdata poly.data #initial data file
pairstyle lj96/cut 1.02 #set LJ style and cutoff
pairmodify shift yes #shift energy at cutoff
paircoeff 1 1 0.37775 0.89 #set LJ parameters
bondstyle harmonic #set bond style
bondcoeff 1 1352.0 0.5 #set bond parameters
anglestyle table spline 181 #set angle style
anglecoeff 1 cgpva.table CGPVA #CGPVA angular potential file
specialbonds 0 0 1.0 #exclude 1-1,1-2 neighbors’ LJ interaction
restart 1000000 poly.restart #restart file
dump 1 all atom 100000 poly.dump #dump file
dumpmodify 1 image yes scale no #dump image values
thermo 100 #interval of statistic information
timestep 0.01 #MD time step
fix 1 all npt 1.0 0.6 1.0 xyz 8.0 8.0 10.0 #NPT & quench
run 40000 #total MD steps

Kindly help.

2

Please, describe better what exactly you actually want to do. Which force-field you want to use, how coarse representation you want, what you want to obtain from your simulation and most of all, where did you get stuck…

3

I want to generate lammps input script for polycarbonate with coarse grained model and i want to make a box using Periodic Boundry condition for polymer, I am not able to understand how to add the parameters to Lammps input script. Kindly help with some example of input.script

4

Do you have any previous experience with LAMMPS?

5

This input is full of syntax errors due to misspelled commands. Please consult the manual for the correct spelling.

7

#filename:“test.in”,

units lj #use reduced units

atom_style angle #set potential style
read_data poly.data #initial data filename

pair_style lj96/cut 1.02 #shift LJ style and cutoff
pair_modify shift yes #shift energy at cutoff
pair_coeff 1 1 0.3775 0.89 #set LJ parameters

bond_style harmonic #set bond style
bond_coeff 1 1352.0 0.5 #set bond parameters

angle_style table spline 181 #set angle style
angle_coeff 1 cg.table CGPVA #CGPVA angular potential file
special_bonds 0 0 1.0 #exclude 1-1,1-2 neighbours’ LJ interaction

restart 100000 poly.restart restart file
dump 1 all atom 100000 poly.dump dump file
dump_modify 1 image yes scale no dump image values

thermo 100 #interval of statistic information
timestep 0.01 #MD time step
fix 1 all npt 1.0 0.6 1.0 xyz 8.0 8.0 10.0 npt & quench
run 40000 #total MD steps

Corrected command

8

This statement makes no sense, since you already provide an example input yourself. What is wrong with that input?

You seem to be misunderstanding what kind of help a forum can provide. I suggest you have a close look at Please Read This First: Guidelines and Suggestions for posting LAMMPS questions and perhaps also Guidelines for posting questions to the LAMMPS forum to get a better understanding of that.

Right now you are creating the impression of somebody that has so little understanding of the task at hand that even asking meaningful questions is difficult. A good way to avoid this is to start with explaining in detail what kind of system you want to simulate (“polymer” is way to general), what kind of steps and simulations you already have done, what your level of experience is with LAMMPS, what version of LAMMPS you are using, what kind of issues/errors you have encountered and especially what are the specific problems with the input you have posted (please note that your input is not quoted correct and thus does not render correctly, see the guidelines post for how to properly quote input files). Please also note, that your input without the data and potential table file is pretty useless for testing.