Use of class II forcefield in lammps for organic molecule

LAMMPS LAMMPS Beginners
1

LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 / CGCMM for EC

100 atoms
100 bonds
170 angles
190 dihedrals
 90 impropers

5 atom types
5 bond types
7 angle types
7 dihedral types
4 improper types

0.00   10.300121381 xlo xhi
0.00   11.167956529 ylo yhi
 0.00    10.945777706 zlo zhi

Masses

1 12.011150 # c2
2 15.999400 # oz
3 12.011150 # cz
4 15.999400 # oo
5 1.007970 # hc

dihedral_coeff 1 -0.6070 0.0060 -0.1441 # oz-c2-c2-oz
dihedral_coeff 2 -3.6896 0.0000 0.0000 # oz-c2-c2-hc
dihedral_coeff 3 -0.1432 0.0617 -0.1083 # hc-c2-c2-hc
dihedral_coeff 4 0.0000 0.0000 -0.1932 # c2-c2-oz-cz
dihedral_coeff 5 0.0000 0.0000 -0.1932 # hc-c2-oz-cz
dihedral_coeff 6 -4.0149 1.8643 0.0000 # c2-oz-cz-oz
dihedral_coeff 7 -4.2342 1.8099 0.0000 # c2-oz-cz-oo
improper_coeff 1 51.6374 0 0 #oz-cz-oz-oo
improper_coeff 2 0.0000 0.0000
improper_coeff 3 0.0000 0.0000
improper_coeff 4 0.0000 0.0000

  1. #BondBond Coeffs

1 0.0000 1.5330 1.5330
2 3.3872 1.5330 1.1010
3 3.3872 1.5330 1.1010
4 5.3316 1.1010 1.1010
5 3.3872 1.5330 1.1010
6 3.3872 1.1010 1.1010
7 3.3872 1.1010 1.1010

BondAngle Coeffs

1 0.0000 0.0000 1.5330 1.5330
2 20.7540 11.4210 1.5330 1.1010
3 20.7540 11.4210 1.5330 1.1010
4 18.1030 18.1030 1.1010 1.1010
5 20.7540 11.4210 1.5330 1.1010
6 20.7540 11.4210 1.1010 1.1010
7 20.7540 11.4210 1.1010 1.1010

AngleAngle Coeffs

1 -1.3199 -1.3199 0.1184 110.7700 110.7700 110.7700
2 -1.3199 -1.3199 0.1184 0.0000 110.7700 110.7700
3 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700
4 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700

  1. #AngleAngleTorsion Coeffs

1 0.0000 0.0000 0.0000
2 -16.1640 0.0000 110.7700
3 -12.5640 110.7700 110.7700
4 -16.1640 0.0000 110.7700
5 -12.5640 110.7700 110.7700
6 -16.1640 110.7700 110.7700
7 -16.1640 110.7700 110.7700

  1. #EndBondTorsion Coeffs

1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5330 1.5330
2 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010
3 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010
5 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
6 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010
7 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010

  1. #MiddleBondTorsion Coeffs

1 0.0000 0.0000 0.0000 1.5330
2 -14.8790 -3.6581 -0.3138 1.5330
3 -14.2610 -0.5322 -0.4864 1.5330
4 -14.8790 -3.6581 -0.3138 1.5330
5 -14.2610 -0.5322 -0.4864 1.5330
6 -14.8790 -3.6581 -0.3138 1.1010
7 -14.8790 -3.6581 -0.3138 1.1010

BondBond13 Coeffs

1 0.0000 1.5330 1.5330
2 0.0000 1.5330 1.1010
3 0.0000 1.1010 1.1010
4 0.0000 1.5330 1.1010
5 0.0000 1.1010 1.1010
6 0.0000 1.5330 1.1010
7 0.0000 1.5330 1.1010

  1. #AngleTorsion Coeffs

1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 0.0000 110.7700
3 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
4 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 0.0000 110.7700
5 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
6 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 110.7700 110.7700
7 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 110.7700 110.7700

while converting file from material studio to lammps. these are data that are obtained but unfortunately in angleangle, bondangle and so on there is no mention about the atom that are related to. how am i suppose to use this in input file also i am finding it hard to use class II cff93 forcefield in the diherdral section if anyone can help that would be great. also i have already looked at Commands — LAMMPS documentation. thank you

2

What you have here is (a part of) a data file with incorrect lines added, bad modifications, and lots of data missing. This is not a LAMMPS input either. How did you create this file?

Those coefficients all apply to the dihedral types, so the corresponding definitions are in the Dihedrals section.

Lots of details about the data file format is in the documentation for read_data. Please have a look.

3

first i made model on material studio then used msi2lmp.exe to convert material studio file into lammps data file. LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 / CGCMM for EC

100 atoms
100 bonds
170 angles
190 dihedrals
 90 impropers

5 atom types
5 bond types
7 angle types
7 dihedral types
4 improper types

-0.041778619    10.300121381 xlo xhi
 0.826056529    11.167956529 ylo yhi
 0.603877706    10.945777706 zlo zhi

Masses

1 12.011150 # c2
2 0.000000 # oz
3 0.000000 # cz
4 0.000000 # oo
5 1.007970 # hc

Pair Coeffs # lj/class2/coul/long

1 0.0540000000 4.0100000000 # c2
2 0.0540000000 4.0100000000 # oz
3 0.0540000000 4.0100000000 # cz
4 0.0540000000 4.0100000000 # oo
5 0.0200000000 2.9950000000 # hc

Bond Coeffs # class2

1 1.5330 299.6700 -501.7700 679.8100 # c2-c2
2 1.5330 299.6700 -501.7700 679.8100 # c2-oz
3 1.1010 341.0000 -691.8900 844.6000 # c2-hc
4 1.1010 341.0000 -691.8900 844.6000 # oz-cz
5 1.1010 341.0000 -691.8900 844.6000 # cz-oo

Angle Coeffs # class2

1 0.0000 0.0000 0.0000 0.0000 # c2-c2-oz
2 110.7700 41.4530 -10.6040 5.1290 # c2-c2-hc
3 110.7700 41.4530 -10.6040 5.1290 # oz-c2-hc
4 107.6600 39.6410 -12.9210 -2.4318 # hc-c2-hc
5 110.7700 41.4530 -10.6040 5.1290 # c2-oz-cz
6 110.7700 41.4530 -10.6040 5.1290 # oz-cz-oz
7 110.7700 41.4530 -10.6040 5.1290 # oz-cz-oo

Dihedral Coeffs # class2

1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# oz-c2-c2-oz
2 0.0000 0.0000 0.0316 0.0000 -0.1781 0.0000# oz-c2-c2-hc
3 -0.2432 0.0000 0.0617 0.0000 -0.1383 0.0000# hc-c2-c2-hc
4 0.0000 0.0000 0.0316 0.0000 -0.1781 0.0000# c2-c2-oz-cz
5 -0.2432 0.0000 0.0617 0.0000 -0.1383 0.0000# hc-c2-oz-cz
6 0.0000 0.0000 0.0316 0.0000 -0.1781 0.0000# c2-oz-cz-oz
7 0.0000 0.0000 0.0316 0.0000 -0.1781 0.0000# c2-oz-cz-oo

Improper Coeffs # class2

1 0.0000 0.0000 # oz-cz-oz-oo
2 0.0000 0.0000
3 0.0000 0.0000
4 0.0000 0.0000

BondBond Coeffs

1 0.0000 1.5330 1.5330
2 3.3872 1.5330 1.1010
3 3.3872 1.5330 1.1010
4 5.3316 1.1010 1.1010
5 3.3872 1.5330 1.1010
6 3.3872 1.1010 1.1010
7 3.3872 1.1010 1.1010

BondAngle Coeffs

1 0.0000 0.0000 1.5330 1.5330
2 20.7540 11.4210 1.5330 1.1010
3 20.7540 11.4210 1.5330 1.1010
4 18.1030 18.1030 1.1010 1.1010
5 20.7540 11.4210 1.5330 1.1010
6 20.7540 11.4210 1.1010 1.1010
7 20.7540 11.4210 1.1010 1.1010

AngleAngle Coeffs

1 -1.3199 -1.3199 0.1184 110.7700 110.7700 110.7700
2 -1.3199 -1.3199 0.1184 0.0000 110.7700 110.7700
3 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700
4 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700

AngleAngleTorsion Coeffs

1 0.0000 0.0000 0.0000
2 -16.1640 0.0000 110.7700
3 -12.5640 110.7700 110.7700
4 -16.1640 0.0000 110.7700
5 -12.5640 110.7700 110.7700
6 -16.1640 110.7700 110.7700
7 -16.1640 110.7700 110.7700

EndBondTorsion Coeffs

1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5330 1.5330
2 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010
3 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010
5 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010
6 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010
7 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5330 1.1010

MiddleBondTorsion Coeffs

1 0.0000 0.0000 0.0000 1.5330
2 -14.8790 -3.6581 -0.3138 1.5330
3 -14.2610 -0.5322 -0.4864 1.5330
4 -14.8790 -3.6581 -0.3138 1.5330
5 -14.2610 -0.5322 -0.4864 1.5330
6 -14.8790 -3.6581 -0.3138 1.1010
7 -14.8790 -3.6581 -0.3138 1.1010

BondBond13 Coeffs

1 0.0000 1.5330 1.5330
2 0.0000 1.5330 1.1010
3 0.0000 1.1010 1.1010
4 0.0000 1.5330 1.1010
5 0.0000 1.1010 1.1010
6 0.0000 1.5330 1.1010
7 0.0000 1.5330 1.1010

AngleTorsion Coeffs

1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 0.0000 110.7700
3 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
4 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 0.0000 110.7700
5 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700
6 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 110.7700 110.7700
7 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 110.7700 110.7700

4

msi2lmp.exe filename -class II -frc cff -print 3 -ignore. i used this command is there anything wrong with this command. can you suggest other command to obtain correct data file. that would be great help thank you

5

So how did you get from the data file listed above (which has the expected syntax) to the one in your original post (which is incorrect)?

6

i just arranged them in order nothing else. the main thing is, after building model in material studio while converting that file to lammps data file, for almost all the forcefield except cvff. data are like this. Does that have to do anything with the command that i used. can you please help me thank you

7

That cannot be. How else would incorrect text show up that cannot have been created by msi2lmp??

I don’t understand what you are asking here. msi2lmp will create a data file according to the force field you are requesting. cvff is a class 1 force field and thus uses different styles than class 2 force fields and those in turn require a different set of sections in the data file. As mentioned before, the format of the data file is discussed at great length and with lots of detail in the documentation for the read_data command. Please have a look.

8

i am just telling the process that i have followed to obtain the data file. i can show the whole process its not possible here.

9

But those don’t answer my questions. It is impossible to create a data file with msi2lmp that has lines like these:

Just telling what you did does not tell us what your exact problems are. I have answered anything that are direct questions. Any statement of the kind “I am struggling with” is not possible to answer without more details and what exactly your struggles are. Note that people here are not mind readers and cannot look over your shoulder to see what you are doing.

Thus, people here can answer specific questions to specific details, but if you need a custom personalized tutoring, you are out of luck.