Hello all,
I want to get the parameters of OPLS-AA force field for a organic molecule(sulfobetaine) and then simulate in LAMMPS.
I know there is a oplsaa.lt file under the installation directory of Moltemplate, but there are so many types to look up and it lacks a lot of variety. So I wonder for such molecule, is there any other ways to obtain the parameters of OPLS-AA force field?
I hope somesone can help me, thanks a lot.
Hello,
There is no link between your question and LAMMPS, and therefore you should ask it in a different forum.
Simon
But I want to set up a model first and then simulate in LAMMPS.
The setup of the model is independent from LAMMPS. For that you need:
All of this has to be done outside of LAMMPS, some parts need to be done manually, others may be automated. Only if you have all this information you can try to build a LAMMPS data or molecule file and then build a system for a simulation.
This forum focuses on LAMMPS itself and not on how to teach people to set up simulations or how to apply force fields. This is usually learned from a tutor or adviser and discussed in forums specific to the force field or the tools related to it. LAMMPS does not have such tools.
Or to explain it with an example: if you buy a car you donāt ask the vendor to teach you how to drive and give you a driverās license? In the simulation business there is no equivalent to a driverās license so people tend to think that can do it without the proper training, but that is a mistake.
From the papers using OPLS-AA force field, I can only find pair coeffs, while other coefficients such as bond coeff and angle coeff are not mentioned. So I wonder how to find these parameters.
You are not looking at the proper publication. There are papers that explain the OPLS-AA force field. Those do include all the information you need. You are looking at a publication that uses the force field. That is different.
An example of how to describe a molecule using oplsaa.lt was posted here.
Search the forum and mailing-list for other moltemplate examples: a good starting point is this one. As pointed out, this forum is really for LAMMPS. Moltemplate is a different software that is used to create input files for LAMMPS.
In fact, I try to set up a model with PACKMOL and complete the topology as well as force field parameters through Moltemplate. I carefully assigned a type to each atom according to the oplsaa.lt file come with Moltemplate, and I checked that the charge of the entire molecule is indeed zero. But when I run nvt after minimization in LAMMPS, it failed at the first step with the error "bond atoms missing. I donāt know what lead to this, is it caused by unreasonable parameters of the force field? I canāt think of any other reason because the rest of the force field parameters Iāve used in other systems, which were also modeled with PACKMOL and the simulation in LAMMPS finally succeeded.
My files are attached.
system.data (134.5 KB)
system.in (1.4 KB)
system.in.charges (44.3 KB)
system.in.settings (95.6 KB)
But there are not all parameters of the force field of the molecule Iām trying to simulate in papers explaining the OPLS-AA force field. I think such paper is hard to find and the structures of polymers Iām trying to simulate are generally complicated.
The input system looks reasonable, even though the atom types for the sulfobetaine seem to be assigned incorrectly: you have a different atom type per atom.
I would use the following strategy:
# Input sample.
wat = new TIP3P [500]
mol = new SLB[10]
cat = new CA
ani = new CL[2]
Render with: moltemplate.sh -overlay-all -pdb my_input.pdb my_script.lt
You should be good to go!
Thatās what I did, but at the first step of nvt it failed with the error "bond atoms missing. 
You assigned bad atom types and possibly also bond types, etc. Have you noticed that, after minimisation, the potential energy increases as crazy? By replacing the atom number with the element symbol, thatās how your molecules look:
The bottom line is that the simulation loses atoms and bonds because the force field is bogus.
EDIT: I have just noticed that molecule 510, represented here, is different from molecules [500:509].
Yes, and I noticed that the energy of this system after minimization is not low enough compared with some of the systems Iāve successfully simulated before.
Besides, the molecule you represented seems a little strange because there shouldnāt be two nitrogen atoms forming a bond. The real polymer would look something like this. And there is only one this polymer in my system.
The molecule I have represented is taken from your DATA file. You better double check how you assigned the atom types, as in the files you shared the hydrogen atoms in the two methyl groups are assigned to @atom:87, which is a carbon in āAlkene RH-C=ā.
I pointed out at the problem, itās up to you to fix it. Donāt waste your time with screenshots, as they do not prove that you set up your polymer correctly.
For instance, the monomers are indeed bonded, but they also have individual molecule identifiers (molid 501:510), while they should have a single one for the entire chain. Check again the instructions on how to set up a polymer in the Moltemplate website.
As for the atom types you mentioned, thatās because the type starts with Calcuim in my data file and the number after the symbol ā#ā corresponds to the real serial number in the oplsaa.lt file.
And I checked the parameters of the force field in my data file and they do match the parameters in the oplsaa.lt file. The only mistake Iāve found is in this āMassesā section, which has been corrected now. But it still canāt work.
While the instruction of my system is set up by PACKMOL, considering that the energy is not enough low after minimization, I doubt the initial structure is unreasonable.
You have made mistakes in the LT files defining your system and/or molecular species, and Moltemplate is assigning atom types accordingly. You will go nowhere by patching some random IDs in the data file. Another error I can spot is that the calcium ion should be assigned type @atom:354 and chlorine ions, type @atom:344.
Also note that posting screenshots of text is utterly useless, other than wasteful. Please share all the files you have used to render your system (PDB from Packmol, LT files with the definition of every species, master LT file with the definition of your system) if you want me to have a look.
I assume you are using the file oplsaa.lt distributed with Moltemplate, so no need to include it.
I wrote the force field of ions with the parameters Iāve successfully simulated before.
H2O.lt (1.8 KB)
ions.lt (549 Bytes)
PolyNIPAM.lt (23.0 KB)
system.lt (264 Bytes)
model.pdb (135.9 KB)
Thanks a lot.
The problem was defining the water, Ca2+, and Cl- with their own atom types: @atom:O, @atom:H, @atom:Ca, and @atom:Cl on top of the atom types already defined in the oplsaa.lt file. This resulted in a mismatch between pair coefficients that produces lost atoms.
I was able to reproduce your error with this definition of the system (LT file):
import "H2O.lt"
import "ions.lt"
import "oplsaa.lt"
import "PolyNIPAM.lt"
# Create the system.
wat=new H2O[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]
With the imports above, the force field settings are specified more than once, as they are inherited by both H2O.lt and oplsaa.lt. The resulting file then must be edited manually after being created by Moltemplate.
You were right: the atom types were assigned correctly for the polymer. Their value was just shifted as 4 new atom types were created before the set defined in OPLS-AA.
If instead of mixing different force fields you describe all the molecular species with OPLS-AA, then the simulation goes just fine. Here are my changes.
First of all, I have assigned a single molid to the polymer residue:
PolyNIPAM inherits OPLSAA {
# Charges will be overwritten.
write("Data Atoms") {
$atom:81_1 $mol @atom:81 0.0 -2.357 -0.245 0.629
$atom:81_2 $mol @atom:81 0.0 -1.194 0.752 0.778
$atom:85_1 $mol @atom:85 0.0 -2.027 -1.242 0.957
$atom:177_1 $mol @atom:177 0.0 -1.743 2.168 0.640
$atom:85_2 $mol @atom:85 0.0 -0.366 0.490 0.103
$atom:180_1 $mol @atom:180 0.0 -1.147 2.943 -0.274
$atom:178_1 $mol @atom:178 0.0 -2.700 2.545 1.293
$atom:171_1 $mol @atom:171 0.0 -1.602 4.322 -0.446
$atom:183_1 $mol @atom:183 0.0 -0.241 2.724 -0.647
$atom:80_1 $mol @atom:80 0.0 -2.662 4.430 -1.547
$atom:80_2 $mol @atom:80 0.0 -0.400 5.227 -0.741
$atom:85_3 $mol @atom:85 0.0 -2.053 4.672 0.501
$atom:85_4 $mol @atom:85 0.0 -3.539 3.796 -1.342
$atom:85_5 $mol @atom:85 0.0 -2.245 4.148 -2.526
$atom:85_6 $mol @atom:85 0.0 -3.006 5.475 -1.612
$atom:85_7 $mol @atom:85 0.0 0.080 4.944 -1.690
$atom:85_8 $mol @atom:85 0.0 0.355 5.185 0.060
$atom:85_9 $mol @atom:85 0.0 -0.737 6.273 -0.826
$atom:85_10 $mol @atom:85 0.0 -3.156 0.050 1.336
$atom:85_11 $mol @atom:85 0.0 -0.808 0.718 1.811
$atom:81_3 $mol @atom:81 0.0 -4.482 -0.662 -0.732
$atom:82_1 $mol @atom:82 0.0 -2.984 -0.308 -0.783
$atom:85_12 $mol @atom:85 0.0 -4.918 0.018 0.014
$atom:177_2 $mol @atom:177 0.0 -2.344 -1.080 -1.873
$atom:180_2 $mol @atom:180 0.0 -1.131 -1.604 -1.620
$atom:178_2 $mol @atom:178 0.0 -2.876 -1.219 -2.965
$atom:171_2 $mol @atom:171 0.0 -0.391 -2.304 -2.661
$atom:183_2 $mol @atom:183 0.0 -0.690 -1.494 -0.727
$atom:80_3 $mol @atom:80 0.0 0.802 -3.029 -2.033
$atom:80_4 $mol @atom:80 0.0 0.094 -1.373 -3.777
$atom:85_13 $mol @atom:85 0.0 -1.054 -3.067 -3.111
$atom:85_14 $mol @atom:85 0.0 0.481 -3.774 -1.288
$atom:85_15 $mol @atom:85 0.0 1.485 -2.319 -1.542
$atom:85_16 $mol @atom:85 0.0 1.368 -3.558 -2.817
$atom:85_17 $mol @atom:85 0.0 0.761 -0.594 -3.382
$atom:85_18 $mol @atom:85 0.0 -0.738 -0.879 -4.300
$atom:85_19 $mol @atom:85 0.0 0.653 -1.964 -4.521
$atom:85_20 $mol @atom:85 0.0 -4.937 -0.363 -1.697
$atom:85_21 $mol @atom:85 0.0 -2.967 0.717 -1.203
$atom:81_4 $mol @atom:81 0.0 -6.422 -2.235 -0.754
$atom:82_2 $mol @atom:82 0.0 -4.928 -2.114 -0.469
$atom:85_22 $mol @atom:85 0.0 -6.565 -1.832 -1.770
$atom:177_3 $mol @atom:177 0.0 -4.663 -2.569 0.992
$atom:180_3 $mol @atom:180 0.0 -3.960 -3.716 1.081
$atom:178_3 $mol @atom:178 0.0 -4.967 -1.904 1.963
$atom:171_3 $mol @atom:171 0.0 -3.354 -4.204 2.319
$atom:183_3 $mol @atom:183 0.0 -4.127 -4.397 0.356
$atom:80_5 $mol @atom:80 0.0 -4.295 -4.572 3.473
$atom:80_6 $mol @atom:80 0.0 -2.271 -3.244 2.828
$atom:85_23 $mol @atom:85 0.0 -2.826 -5.135 2.038
$atom:85_24 $mol @atom:85 0.0 -4.973 -5.396 3.211
$atom:85_25 $mol @atom:85 0.0 -4.909 -3.718 3.794
$atom:85_26 $mol @atom:85 0.0 -3.683 -4.896 4.331
$atom:85_27 $mol @atom:85 0.0 -2.695 -2.272 3.123
$atom:85_28 $mol @atom:85 0.0 -1.484 -3.073 2.079
$atom:85_29 $mol @atom:85 0.0 -1.791 -3.686 3.717
$atom:85_30 $mol @atom:85 0.0 -6.661 -3.312 -0.799
$atom:85_31 $mol @atom:85 0.0 -4.422 -2.764 -1.206
$atom:81_5 $mol @atom:81 0.0 -8.861 -2.101 -0.226
$atom:82_3 $mol @atom:82 0.0 -7.457 -1.604 0.194
$atom:85_32 $mol @atom:85 0.0 -8.826 -3.186 -0.048
$atom:177_4 $mol @atom:177 0.0 -7.425 -0.036 0.256
$atom:180_4 $mol @atom:180 0.0 -6.870 0.431 1.405
$atom:178_4 $mol @atom:178 0.0 -8.004 0.653 -0.558
$atom:171_4 $mol @atom:171 0.0 -7.168 1.765 1.912
$atom:183_4 $mol @atom:183 0.0 -6.797 -0.317 2.080
$atom:80_7 $mol @atom:80 0.0 -8.664 2.017 2.147
$atom:80_8 $mol @atom:80 0.0 -6.545 2.857 1.036
$atom:85_33 $mol @atom:85 0.0 -6.669 1.831 2.899
$atom:85_34 $mol @atom:85 0.0 -9.114 1.252 2.800
$atom:85_35 $mol @atom:85 0.0 -9.236 2.024 1.205
$atom:85_36 $mol @atom:85 0.0 -8.786 3.001 2.625
$atom:85_37 $mol @atom:85 0.0 -7.002 2.900 0.037
$atom:85_38 $mol @atom:85 0.0 -5.460 2.706 0.913
$atom:85_39 $mol @atom:85 0.0 -6.693 3.836 1.521
$atom:85_40 $mol @atom:85 0.0 -9.602 -1.708 0.496
$atom:85_41 $mol @atom:85 0.0 -7.328 -2.030 1.207
$atom:81_6 $mol @atom:81 0.0 -10.877 -2.392 -1.741
$atom:82_4 $mol @atom:82 0.0 -9.440 -1.848 -1.636
$atom:85_42 $mol @atom:85 0.0 -11.441 -2.051 -0.857
$atom:177_5 $mol @atom:177 0.0 -8.631 -2.553 -2.770
$atom:180_5 $mol @atom:180 0.0 -8.499 -1.785 -3.863
$atom:178_5 $mol @atom:178 0.0 -8.181 -3.684 -2.688
$atom:171_5 $mol @atom:171 0.0 -7.938 -2.258 -5.119
$atom:183_5 $mol @atom:183 0.0 -9.049 -0.943 -3.902
$atom:80_9 $mol @atom:80 0.0 -8.792 -3.342 -5.780
$atom:80_10 $mol @atom:80 0.0 -6.470 -2.687 -5.003
$atom:85_43 $mol @atom:85 0.0 -7.963 -1.383 -5.795
$atom:85_44 $mol @atom:85 0.0 -9.825 -2.995 -5.943
$atom:85_45 $mol @atom:85 0.0 -8.838 -4.264 -5.179
$atom:85_46 $mol @atom:85 0.0 -8.360 -3.594 -6.761
$atom:85_47 $mol @atom:85 0.0 -6.361 -3.605 -4.407
$atom:85_48 $mol @atom:85 0.0 -5.850 -1.903 -4.541
$atom:85_49 $mol @atom:85 0.0 -6.071 -2.887 -6.011
$atom:85_50 $mol @atom:85 0.0 -11.356 -1.921 -2.619
$atom:85_51 $mol @atom:85 0.0 -9.494 -0.756 -1.795
$atom:81_7 $mol @atom:81 0.0 -12.476 -4.326 -2.296
$atom:82_5 $mol @atom:82 0.0 -11.042 -3.918 -1.914
$atom:85_52 $mol @atom:85 0.0 -12.606 -4.028 -3.347
$atom:177_6 $mol @atom:177 0.0 -10.631 -4.675 -0.614
$atom:180_6 $mol @atom:180 0.0 -9.796 -5.703 -0.861
$atom:178_6 $mol @atom:178 0.0 -11.127 -4.453 0.474
$atom:171_6 $mol @atom:171 0.0 -9.186 -6.529 0.183
$atom:183_6 $mol @atom:183 0.0 -9.206 -5.554 -1.669
$atom:80_11 $mol @atom:80 0.0 -10.225 -7.315 0.995
$atom:80_12 $mol @atom:80 0.0 -8.204 -5.783 1.100
$atom:85_53 $mol @atom:85 0.0 -8.602 -7.290 -0.368
$atom:85_54 $mol @atom:85 0.0 -10.889 -7.898 0.339
$atom:85_55 $mol @atom:85 0.0 -10.843 -6.658 1.625
$atom:85_56 $mol @atom:85 0.0 -9.699 -8.020 1.659
$atom:85_57 $mol @atom:85 0.0 -8.739 -5.060 1.735
$atom:85_58 $mol @atom:85 0.0 -7.431 -5.245 0.530
$atom:85_59 $mol @atom:85 0.0 -7.700 -6.510 1.757
$atom:85_60 $mol @atom:85 0.0 -12.525 -5.430 -2.285
$atom:85_61 $mol @atom:85 0.0 -10.438 -4.244 -2.777
$atom:81_8 $mol @atom:81 0.0 -14.920 -4.584 -1.600
$atom:82_6 $mol @atom:82 0.0 -13.632 -3.752 -1.465
$atom:85_62 $mol @atom:85 0.0 -14.649 -5.586 -1.247
$atom:177_7 $mol @atom:177 0.0 -13.893 -2.285 -1.914
$atom:180_7 $mol @atom:180 0.0 -13.965 -1.422 -0.889
$atom:178_7 $mol @atom:178 0.0 -13.974 -1.956 -3.082
$atom:171_7 $mol @atom:171 0.0 -14.239 0.001 -1.025
$atom:183_7 $mol @atom:183 0.0 -13.577 -1.708 -0.004
$atom:80_13 $mol @atom:80 0.0 -15.680 0.246 -1.480
$atom:80_14 $mol @atom:80 0.0 -13.267 0.807 -1.893
$atom:85_63 $mol @atom:85 0.0 -14.156 0.414 -0.002
$atom:85_64 $mol @atom:85 0.0 -16.408 -0.251 -0.821
$atom:85_65 $mol @atom:85 0.0 -15.849 -0.114 -2.507
$atom:85_66 $mol @atom:85 0.0 -15.890 1.327 -1.461
$atom:85_67 $mol @atom:85 0.0 -13.268 0.469 -2.940
$atom:85_68 $mol @atom:85 0.0 -12.239 0.760 -1.513
$atom:85_69 $mol @atom:85 0.0 -13.597 1.859 -1.881
$atom:85_70 $mol @atom:85 0.0 -15.637 -4.195 -0.859
$atom:85_71 $mol @atom:85 0.0 -13.362 -3.817 -0.395
$atom:81_9 $mol @atom:81 0.0 -17.064 -5.395 -2.685
$atom:82_7 $mol @atom:82 0.0 -15.684 -4.733 -2.934
$atom:85_72 $mol @atom:85 0.0 -17.540 -4.759 -1.921
$atom:177_8 $mol @atom:177 0.0 -14.870 -5.540 -3.996
$atom:180_8 $mol @atom:180 0.0 -14.373 -4.756 -4.977
$atom:178_8 $mol @atom:178 0.0 -14.748 -6.750 -3.981
$atom:171_8 $mol @atom:171 0.0 -13.393 -5.268 -5.940
$atom:183_8 $mol @atom:183 0.0 -14.174 -3.807 -4.679
$atom:80_15 $mol @atom:80 0.0 -14.106 -6.091 -7.020
$atom:80_16 $mol @atom:80 0.0 -12.175 -6.042 -5.407
$atom:85_73 $mol @atom:85 0.0 -12.988 -4.367 -6.439
$atom:85_74 $mol @atom:85 0.0 -14.926 -5.528 -7.494
$atom:85_75 $mol @atom:85 0.0 -14.530 -7.019 -6.606
$atom:85_76 $mol @atom:85 0.0 -13.392 -6.372 -7.812
$atom:85_77 $mol @atom:85 0.0 -12.467 -7.007 -4.964
$atom:85_78 $mol @atom:85 0.0 -11.600 -5.477 -4.663
$atom:85_79 $mol @atom:85 0.0 -11.507 -6.251 -6.259
$atom:85_80 $mol @atom:85 0.0 -17.675 -5.258 -3.598
$atom:85_81 $mol @atom:85 0.0 -15.938 -3.724 -3.313
$atom:81_10 $mol @atom:81 0.0 -18.749 -7.194 -2.096
$atom:82_8 $mol @atom:82 0.0 -17.248 -6.883 -2.287
$atom:85_82 $mol @atom:85 0.0 -19.267 -6.796 -2.989
$atom:177_9 $mol @atom:177 0.0 -16.454 -7.269 -0.999
$atom:180_9 $mol @atom:180 0.0 -15.335 -7.967 -1.254
$atom:178_9 $mol @atom:178 0.0 -16.762 -6.899 0.120
$atom:171_9 $mol @atom:171 0.0 -14.367 -8.387 -0.248
$atom:183_9 $mol @atom:183 0.0 -15.240 -8.331 -2.192
$atom:80_17 $mol @atom:80 0.0 -14.904 -9.451 0.715
$atom:80_18 $mol @atom:80 0.0 -13.725 -7.242 0.549
$atom:85_83 $mol @atom:85 0.0 -13.545 -8.861 -0.817
$atom:85_84 $mol @atom:85 0.0 -15.290 -10.333 0.182
$atom:85_85 $mol @atom:85 0.0 -15.717 -9.064 1.350
$atom:85_86 $mol @atom:85 0.0 -14.087 -9.788 1.373
$atom:85_87 $mol @atom:85 0.0 -14.468 -6.647 1.100
$atom:85_88 $mol @atom:85 0.0 -13.139 -6.565 -0.089
$atom:85_89 $mol @atom:85 0.0 -13.036 -7.679 1.290
$atom:85_90 $mol @atom:85 0.0 -18.877 -8.292 -2.150
$atom:85_91 $mol @atom:85 0.0 -16.939 -7.505 -3.147
$atom:80_19 $mol @atom:80 0.0 -20.999 -7.206 -1.036
$atom:82_9 $mol @atom:82 0.0 -19.540 -6.757 -0.843
$atom:85_92 $mol @atom:85 0.0 -21.046 -8.300 -1.156
$atom:85_93 $mol @atom:85 0.0 -21.439 -6.747 -1.936
$atom:177_10 $mol @atom:177 0.0 -19.578 -5.207 -0.628
$atom:180_10 $mol @atom:180 0.0 -19.061 -4.828 0.557
$atom:178_10 $mol @atom:178 0.0 -20.185 -4.465 -1.375
$atom:171_10 $mol @atom:171 0.0 -18.878 -3.426 0.994
$atom:183_10 $mol @atom:183 0.0 -18.342 -5.450 0.901
$atom:80_20 $mol @atom:80 0.0 -19.984 -2.451 0.558
$atom:80_21 $mol @atom:80 0.0 -17.509 -2.857 0.610
$atom:85_94 $mol @atom:85 0.0 -18.906 -3.470 2.099
$atom:85_95 $mol @atom:85 0.0 -20.991 -2.887 0.651
$atom:85_96 $mol @atom:85 0.0 -19.829 -2.132 -0.485
$atom:85_97 $mol @atom:85 0.0 -19.955 -1.550 1.193
$atom:85_98 $mol @atom:85 0.0 -17.405 -2.773 -0.482
$atom:85_99 $mol @atom:85 0.0 -16.684 -3.475 0.993
$atom:85_100 $mol @atom:85 0.0 -17.407 -1.849 1.043
$atom:85_101 $mol @atom:85 0.0 -21.621 -6.939 -0.168
$atom:85_102 $mol @atom:85 0.0 -19.160 -7.294 0.044
}
write("Data Bond List") {
$bond:id1 $atom:81_1 $atom:81_2
$bond:id2 $atom:81_1 $atom:85_1
$bond:id3 $atom:81_1 $atom:85_10
$bond:id4 $atom:81_1 $atom:82_1
$bond:id5 $atom:81_2 $atom:177_1
$bond:id6 $atom:81_2 $atom:85_2
$bond:id7 $atom:81_2 $atom:85_11
$bond:id8 $atom:177_1 $atom:180_1
$bond:id9 $atom:177_1 $atom:178_1
$bond:id10 $atom:180_1 $atom:171_1
$bond:id11 $atom:180_1 $atom:183_1
$bond:id12 $atom:171_1 $atom:80_1
$bond:id13 $atom:171_1 $atom:80_2
$bond:id14 $atom:85_3 $atom:171_1
$bond:id15 $atom:85_4 $atom:80_1
$bond:id16 $atom:85_5 $atom:80_1
$bond:id17 $atom:85_6 $atom:80_1
$bond:id18 $atom:85_7 $atom:80_2
$bond:id19 $atom:85_8 $atom:80_2
$bond:id20 $atom:85_9 $atom:80_2
$bond:id21 $atom:81_3 $atom:82_1
$bond:id22 $atom:81_3 $atom:85_12
$bond:id23 $atom:81_3 $atom:85_20
$bond:id24 $atom:81_3 $atom:82_2
$bond:id25 $atom:177_2 $atom:82_1
$bond:id26 $atom:85_21 $atom:82_1
$bond:id27 $atom:177_2 $atom:180_2
$bond:id28 $atom:177_2 $atom:178_2
$bond:id29 $atom:180_2 $atom:171_2
$bond:id30 $atom:180_2 $atom:183_2
$bond:id31 $atom:171_2 $atom:80_3
$bond:id32 $atom:171_2 $atom:80_4
$bond:id33 $atom:85_13 $atom:171_2
$bond:id34 $atom:85_14 $atom:80_3
$bond:id35 $atom:85_15 $atom:80_3
$bond:id36 $atom:85_16 $atom:80_3
$bond:id37 $atom:85_17 $atom:80_4
$bond:id38 $atom:85_18 $atom:80_4
$bond:id39 $atom:85_19 $atom:80_4
$bond:id40 $atom:81_4 $atom:82_2
$bond:id41 $atom:81_4 $atom:85_22
$bond:id42 $atom:81_4 $atom:85_30
$bond:id43 $atom:81_4 $atom:82_3
$bond:id44 $atom:177_3 $atom:82_2
$bond:id45 $atom:85_31 $atom:82_2
$bond:id46 $atom:177_3 $atom:180_3
$bond:id47 $atom:177_3 $atom:178_3
$bond:id48 $atom:180_3 $atom:171_3
$bond:id49 $atom:180_3 $atom:183_3
$bond:id50 $atom:171_3 $atom:80_5
$bond:id51 $atom:171_3 $atom:80_6
$bond:id52 $atom:85_23 $atom:171_3
$bond:id53 $atom:85_24 $atom:80_5
$bond:id54 $atom:85_25 $atom:80_5
$bond:id55 $atom:85_26 $atom:80_5
$bond:id56 $atom:85_27 $atom:80_6
$bond:id57 $atom:85_28 $atom:80_6
$bond:id58 $atom:85_29 $atom:80_6
$bond:id59 $atom:81_5 $atom:82_3
$bond:id60 $atom:81_5 $atom:85_32
$bond:id61 $atom:81_5 $atom:85_40
$bond:id62 $atom:81_5 $atom:82_4
$bond:id63 $atom:177_4 $atom:82_3
$bond:id64 $atom:85_41 $atom:82_3
$bond:id65 $atom:177_4 $atom:180_4
$bond:id66 $atom:177_4 $atom:178_4
$bond:id67 $atom:180_4 $atom:171_4
$bond:id68 $atom:180_4 $atom:183_4
$bond:id69 $atom:171_4 $atom:80_7
$bond:id70 $atom:171_4 $atom:80_8
$bond:id71 $atom:85_33 $atom:171_4
$bond:id72 $atom:85_34 $atom:80_7
$bond:id73 $atom:85_35 $atom:80_7
$bond:id74 $atom:85_36 $atom:80_7
$bond:id75 $atom:85_37 $atom:80_8
$bond:id76 $atom:85_38 $atom:80_8
$bond:id77 $atom:85_39 $atom:80_8
$bond:id78 $atom:81_6 $atom:82_4
$bond:id79 $atom:81_6 $atom:85_42
$bond:id80 $atom:81_6 $atom:85_50
$bond:id81 $atom:81_6 $atom:82_5
$bond:id82 $atom:177_5 $atom:82_4
$bond:id83 $atom:85_51 $atom:82_4
$bond:id84 $atom:177_5 $atom:180_5
$bond:id85 $atom:177_5 $atom:178_5
$bond:id86 $atom:180_5 $atom:171_5
$bond:id87 $atom:180_5 $atom:183_5
$bond:id88 $atom:171_5 $atom:80_9
$bond:id89 $atom:171_5 $atom:80_10
$bond:id90 $atom:85_43 $atom:171_5
$bond:id91 $atom:85_44 $atom:80_9
$bond:id92 $atom:85_45 $atom:80_9
$bond:id93 $atom:85_46 $atom:80_9
$bond:id94 $atom:85_47 $atom:80_10
$bond:id95 $atom:85_48 $atom:80_10
$bond:id96 $atom:85_49 $atom:80_10
$bond:id97 $atom:81_7 $atom:82_5
$bond:id98 $atom:81_7 $atom:85_52
$bond:id99 $atom:81_7 $atom:85_60
$bond:id100 $atom:81_7 $atom:82_6
$bond:id101 $atom:177_6 $atom:82_5
$bond:id102 $atom:85_61 $atom:82_5
$bond:id103 $atom:177_6 $atom:180_6
$bond:id104 $atom:177_6 $atom:178_6
$bond:id105 $atom:180_6 $atom:171_6
$bond:id106 $atom:180_6 $atom:183_6
$bond:id107 $atom:171_6 $atom:80_11
$bond:id108 $atom:171_6 $atom:80_12
$bond:id109 $atom:85_53 $atom:171_6
$bond:id110 $atom:85_54 $atom:80_11
$bond:id111 $atom:85_55 $atom:80_11
$bond:id112 $atom:85_56 $atom:80_11
$bond:id113 $atom:85_57 $atom:80_12
$bond:id114 $atom:85_58 $atom:80_12
$bond:id115 $atom:85_59 $atom:80_12
$bond:id116 $atom:81_8 $atom:82_6
$bond:id117 $atom:81_8 $atom:85_62
$bond:id118 $atom:81_8 $atom:85_70
$bond:id119 $atom:81_8 $atom:82_7
$bond:id120 $atom:177_7 $atom:82_6
$bond:id121 $atom:85_71 $atom:82_6
$bond:id122 $atom:177_7 $atom:180_7
$bond:id123 $atom:177_7 $atom:178_7
$bond:id124 $atom:180_7 $atom:171_7
$bond:id125 $atom:180_7 $atom:183_7
$bond:id126 $atom:171_7 $atom:80_13
$bond:id127 $atom:171_7 $atom:80_14
$bond:id128 $atom:85_63 $atom:171_7
$bond:id129 $atom:85_64 $atom:80_13
$bond:id130 $atom:85_65 $atom:80_13
$bond:id131 $atom:85_66 $atom:80_13
$bond:id132 $atom:85_67 $atom:80_14
$bond:id133 $atom:85_68 $atom:80_14
$bond:id134 $atom:85_69 $atom:80_14
$bond:id135 $atom:81_9 $atom:82_7
$bond:id136 $atom:81_9 $atom:85_72
$bond:id137 $atom:81_9 $atom:85_80
$bond:id138 $atom:81_9 $atom:82_8
$bond:id139 $atom:177_8 $atom:82_7
$bond:id140 $atom:85_81 $atom:82_7
$bond:id141 $atom:177_8 $atom:180_8
$bond:id142 $atom:177_8 $atom:178_8
$bond:id143 $atom:180_8 $atom:171_8
$bond:id144 $atom:180_8 $atom:183_8
$bond:id145 $atom:171_8 $atom:80_15
$bond:id146 $atom:171_8 $atom:80_16
$bond:id147 $atom:85_73 $atom:171_8
$bond:id148 $atom:85_74 $atom:80_15
$bond:id149 $atom:85_75 $atom:80_15
$bond:id150 $atom:85_76 $atom:80_15
$bond:id151 $atom:85_77 $atom:80_16
$bond:id152 $atom:85_78 $atom:80_16
$bond:id153 $atom:85_79 $atom:80_16
$bond:id154 $atom:81_10 $atom:82_8
$bond:id155 $atom:81_10 $atom:85_82
$bond:id156 $atom:81_10 $atom:85_90
$bond:id157 $atom:81_10 $atom:82_9
$bond:id158 $atom:177_9 $atom:82_8
$bond:id159 $atom:85_91 $atom:82_8
$bond:id160 $atom:177_9 $atom:180_9
$bond:id161 $atom:177_9 $atom:178_9
$bond:id162 $atom:180_9 $atom:171_9
$bond:id163 $atom:180_9 $atom:183_9
$bond:id164 $atom:171_9 $atom:80_17
$bond:id165 $atom:171_9 $atom:80_18
$bond:id166 $atom:85_83 $atom:171_9
$bond:id167 $atom:85_84 $atom:80_17
$bond:id168 $atom:85_85 $atom:80_17
$bond:id169 $atom:85_86 $atom:80_17
$bond:id170 $atom:85_87 $atom:80_18
$bond:id171 $atom:85_88 $atom:80_18
$bond:id172 $atom:85_89 $atom:80_18
$bond:id173 $atom:80_19 $atom:82_9
$bond:id174 $atom:85_92 $atom:80_19
$bond:id175 $atom:85_93 $atom:80_19
$bond:id176 $atom:85_101 $atom:80_19
$bond:id177 $atom:177_10 $atom:82_9
$bond:id178 $atom:85_102 $atom:82_9
$bond:id179 $atom:177_10 $atom:180_10
$bond:id180 $atom:177_10 $atom:178_10
$bond:id181 $atom:180_10 $atom:171_10
$bond:id182 $atom:180_10 $atom:183_10
$bond:id183 $atom:171_10 $atom:80_20
$bond:id184 $atom:171_10 $atom:80_21
$bond:id185 $atom:85_94 $atom:171_10
$bond:id186 $atom:85_95 $atom:80_20
$bond:id187 $atom:85_96 $atom:80_20
$bond:id188 $atom:85_97 $atom:80_20
$bond:id189 $atom:85_98 $atom:80_21
$bond:id190 $atom:85_99 $atom:80_21
$bond:id191 $atom:85_100 $atom:80_21
}
} # end of "PolyNIPAM inherits OPLSAA" type definition
No need to specify the charges, as they will be overwritten.
Then I created a master file for the simulation. This file contains also the macros defining SPC water, Ca and Cl ions, but of course these species could be saved in separate files and imported. I put everything together for the sake of space.
# Use the OPLS-AA force field for all species.
import "oplsaa.lt"
import "PolyNIPAM.lt"
# Define the SPC water and ions as in the OPLS-AA
Ca inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000
}
}
Cl inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000
}
}
H2O inherits OPLSAA {
write("Data Atoms"){
$atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000
$atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590
$atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
}
write("Data Bond List") {
$bond:OH1 $atom:O $atom:H1
$bond:OH2 $atom:O $atom:H2
}
}
# Create the system.
wat=new H2O[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]
# Periodic boundary conditions:
write_once("Data Boundary"){
0 26 xlo xhi
0 26 ylo yhi
0 26 zlo zhi
}
# Define the input variables.
write_once("In Init"){
# Input variables.
variable ts equal 1 # timestep
variable temp equal 298.15 # equilibrium temperature
variable p equal 1. # equilibrium pressure
# PBC (set them before the creation of the box).
boundary p p p
neighbor 3 bin
}
# Let's go, Pickacku!
write_once("In Run"){
dump 33 all dcd 500 sample01.dcd
dump_modify 33 unwrap yes
group watergroup type 76 77
velocity all create \$\{temp\} 12345
timestep \$\{ts\}
thermo 1000
thermo_style custom step temp press pe ke etotal atoms lx ly lz vol density
thermo_modify flush yes
minimize .01 .001 1000 100000
write_data min.data
fix 0 watergroup shake 0.0001 20 0 b 1 a 1
fix 1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt) drag 2
run 500000
unfix 1
fix 1 all npt temp \$\{temp\} \$\{temp\} \$(100*dt) iso \$p \$p \$(1000*dt) drag 2
run 500000
unfix 1
write_data Equil.data
fix 1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt) drag 2
run 1000000
write_data final.data
}
Render with:
moltemplate.sh -overlay-all -pdb model.pdb sample02.lt
Run with:
mpirun -np 4 lmp_2Aug23 -in sample01.in -l sample01.log
In this case, the simulation quickly reaches thermal equilibrium:
I hope this is a helpful reference for anyone willing to use the OPLS-AA force field in combination with a PDB containing the initial guess of a molecular system.
@hothello How about you convert this use case into some kind of a moltemplate howto for the LAMMPS manual?
Sure, happy to help with the manual. @jewettaij did a great job with making available the OPLS-AA force field in the LT format. Defining the molecular topology is quite straightforward, as one only has to assign the atom types and specify the list of bonds: the rest is all taken care by Moltemplate.
We take this offline (I will also need to contact you for the paper on CG alkanes!).
