Running the Build¶
Now, in our working directory my_dgeba_pacm/4-pacm-dgeba-epoxy-thermoset/, if you haven’t already, go ahead and launch via ./run.sh.
$ ./run.sh
As the two htpolynet run commands indicate, standard output is being redirected from the console to the file console.log.
First the banner and the runtime initialization messages:
INFO>
INFO> HTPolyNet 1.0.8
INFO> https://abramsgroup.github.io/HTPolyNet/
INFO>
INFO> Ming Huang
INFO> mh3429@dragons.drexel.edu
INFO>
INFO> Cameron F. Abrams
INFO> cfa22@drexel.edu
INFO>
INFO> Supported in part by Grants W911NF-17-2-0227
INFO> and W911NF-12-R-0011 from the US Army Research Lab
INFO>
INFO> Please cite the HTPolyNet paper:
INFO>
INFO> Ming Huang and Cameron F. Abrams, HTPolyNet: A general
INFO> system generator for all-atom molecular simulations of
INFO> amorphous crosslinked polymers, SoftwareX, vol. 21,
INFO> pp. 101303, 2023 (doi:10.1016/j.softx.2022.101303)
INFO>
INFO> ******************** HTPolyNet runtime begins *********************
INFO> User library is /home/cfa/htpolynet-tutorials/1.0.8/4-pacm-dgeba-epoxy-thermoset/lib
INFO> New project in /home/cfa/htpolynet-tutorials/1.0.8/4-pacm-dgeba-epoxy-thermoset/proj-0
INFO> *************************** Ambertools: ***************************
INFO> ******************** antechamber (ver. 22.0) *********************
INFO> ******************** tleap (ver. 22.0) *********************
INFO> ******************** parmchk2 (ver. 22.0) *********************
INFO> Configuration: DGEPAC.yaml
Then a description of all the molecules that need to be created:
INFO> *********** Templates in proj-0/molecules/parameterized ***********
INFO> 22 molecules detected in DGEPAC.yaml
INFO> explicit: 5
INFO> implied by stereochemistry: 6
INFO> implied by symmetry: 11
INFO> AmberTools> generating GAFF parameters from PAC.mol2
INFO> PAC: 210.36 g/mol
INFO> AmberTools> generating GAFF parameters from DGE.mol2
INFO> DGE: 344.43 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N1-C1~DGE.mol2
INFO> PAC~N1-C1~DGE: 552.78 g/mol
INFO> AmberTools> generating GAFF parameters from DGEC.mol2
INFO> DGEC: 342.42 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N1-C1~DGE-C1~DGE.mol2
INFO> PAC~N1-C1~DGE-C1~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N1-C2~DGE.mol2
INFO> PAC~N1-C2~DGE: 552.78 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N1-C2~DGE~N1-C1~DGE.mol2
INFO> PAC~N1-C2~DGE~N1-C1~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N2-C1~DGE.mol2
INFO> PAC~N2-C1~DGE: 552.78 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N2-C1~DGE~N2-C1~DGE.mol2
INFO> PAC~N2-C1~DGE~N2-C1~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N2-C2~DGE.mol2
INFO> PAC~N2-C2~DGE: 552.78 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N2-C2~DGE~N2-C1~DGE.mol2
INFO> PAC~N2-C2~DGE~N2-C1~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N1-C1~DGE~N1-C2~DGE.mol2
INFO> PAC~N1-C1~DGE~N1-C2~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from DGEC-1.mol2
INFO> DGEC-1: 342.42 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N1-C2~DGE~N1-C2~DGE.mol2
INFO> PAC~N1-C2~DGE~N1-C2~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N2-C1~DGE~N2-C2~DGE.mol2
INFO> PAC~N2-C1~DGE~N2-C2~DGE: 895.19 g/mol
INFO> AmberTools> generating GAFF parameters from PAC~N2-C2~DGE~N2-C2~DGE.mol2
INFO> PAC~N2-C2~DGE~N2-C2~DGE: 895.19 g/mol
INFO> Generated 22 molecule templates
INFO> Initial composition is DGE 200, PAC 100
INFO> 100% conversion is 400 bonds
Notice that the symmetry-equivalent atoms in both monomers result in a total of 12 unique cure reactions forming secondary and tertiary amines, as well as two capping reactions for DGEBA. Now the initial construction of the system and its densification are next:
INFO> ************** Initialization in proj-0/systems/init **************
INFO> Topology "init.top" in proj-0/systems/init
INFO> Initial density: 300.0 kg/m^3
INFO> Total mass: 1.493e-22 kg
INFO> Box aspect ratio: 1.0 x 1.0 x 1.0
INFO> Initial box side lengths: 7.925 nm x 7.925 nm x 7.925 nm
INFO> Coordinates "init.gro" in proj-0/systems/init
INFO> Extended attributes "init.grx" in proj-0/systems/init
INFO> ********** Densification in proj-0/systems/densification **********
INFO> Running Gromacs: minimization
INFO> Running Gromacs: nvt ensemble; 10.00 ps, 300.00 K
INFO> Running Gromacs: npt ensemble; 300.00 ps, 300.00 K, 10.00 bar
INFO> Current box side lengths: 5.225 nm x 5.225 nm x 5.225 nm
INFO> Density 1046.77
INFO> Running-average-Density 875.31
INFO> Rolling-10-average-Density 1044.65
INFO> Densified coordinates in proj-0/systems/densification/densified-npt.gro
INFO> **************** Precure in proj-0/systems/precure ****************
INFO> Running Gromacs: npt ensemble; 200.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.219 nm x 5.219 nm x 5.219 nm
INFO> Density 1050.62
INFO> Running-average-Density 1047.96
INFO> Rolling-10-average-Density 1050.99
INFO> Annealing: 5 points for 2 cycles over 160 ps
INFO> Annealed coordinates in annealed.gro
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.224 nm x 5.224 nm x 5.224 nm
INFO> Density 1047.39
INFO> Running-average-Density 1048.71
INFO> Rolling-10-average-Density 1049.57
Note that we achieve a pretty good initial density for this liquid of about 1.05 g/cc. Now the CURE algorithm begins, seeking to form 380 out of the total possible 400 bonds:
INFO> ********* Connect-Update-Relax-Equilibrate (CURE) begins **********
INFO> Attempting to form 380 bonds
INFO> ~~~~~~~~~~~~~~~~~~~~~~~ Iteration 1 begins ~~~~~~~~~~~~~~~~~~~~~~~~
INFO> Bond search using radius 0.5 nm initiated
The run then enters the CURE iterations. The console output shows that 121 bonds form in just those first two iterations:
INFO> ~~~~~~~~~~~~~~~~~~~~~~~ Iteration 1 begins ~~~~~~~~~~~~~~~~~~~~~~~~
INFO> Bond search using radius 0.5 nm initiated
INFO> Iteration 1 will generate 71 new bonds
INFO> Step "cure_relax" initiated on 71 distances (max 0.478 nm)
INFO> Stage Max-distance (nm) Max-1-4-distance (nm)
INFO> 1 0.418 0.639
INFO> 2 0.349 0.588
INFO> 3 0.279 0.526
INFO> 4 0.224 0.461
INFO> 5 0.156 0.405
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.228 nm x 5.228 nm x 5.228 nm
INFO> Density 1043.18
INFO> Running-average-Density 1022.51
INFO> Rolling-10-average-Density 1042.26
INFO> Iteration 1 current conversion 0.177 or 71 bonds
INFO> ~~~~~~~~~~~~~~~~~~~~~~~ Iteration 2 begins ~~~~~~~~~~~~~~~~~~~~~~~~
INFO> Bond search using radius 0.5 nm initiated
INFO> Iteration 2 will generate 50 new bonds
INFO> Step "cure_relax" initiated on 50 distances (max 0.489 nm)
INFO> Stage Max-distance (nm) Max-1-4-distance (nm)
INFO> 1 0.448 0.662
INFO> 2 0.362 0.586
INFO> 3 0.325 0.546
INFO> 4 0.257 0.487
INFO> 5 0.212 0.446
INFO> 6 0.157 0.403
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.216 nm x 5.216 nm x 5.216 nm
INFO> Density 1049.56
INFO> Running-average-Density 1025.18
INFO> Rolling-10-average-Density 1045.13
INFO> Iteration 2 current conversion 0.302 or 121 bonds
This rate of bond formation doesn’t last, though. It gets harder and harder to find potential partners the deeper into the cure we go. By the end, this build required 32 CURE iterations. The console output for the last two is below, and we see both required pre-bond dragging before bond formation and relaxation:
INFO> ~~~~~~~~~~~~~~~~~~~~~~~ Iteration 31 begins ~~~~~~~~~~~~~~~~~~~~~~~
INFO> Bond search using radius 0.5 nm initiated
INFO> Iteration 31 will generate 5 new bonds
INFO> Step "cure_drag" initiated on 5 distances (max 0.994 nm)
INFO> Stage Max-distance (nm)
INFO> 1 0.926
INFO> 2 0.886
INFO> 3 0.817
INFO> 4 0.764
INFO> 5 0.707
INFO> 6 0.653
INFO> 7 0.593
INFO> 8 0.536
INFO> 9 0.478
INFO> 10 0.423
INFO> 11 0.361
INFO> 12 0.303
INFO> Step "cure_relax" initiated on 5 distances (max 0.303 nm)
INFO> Stage Max-distance (nm) Max-1-4-distance (nm)
INFO> 1 0.261 0.499
INFO> 2 0.207 0.444
INFO> 3 0.154 0.400
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.199 nm x 5.199 nm x 5.199 nm
INFO> Density 1053.87
INFO> Running-average-Density 1040.71
INFO> Rolling-10-average-Density 1055.13
INFO> Iteration 31 current conversion 0.945 or 378 bonds
INFO> ~~~~~~~~~~~~~~~~~~~~~~~ Iteration 32 begins ~~~~~~~~~~~~~~~~~~~~~~~
INFO> Bond search using radius 0.5 nm initiated
INFO> Iteration 32 will generate 2 new bonds
INFO> Step "cure_drag" initiated on 2 distances (max 0.720 nm)
INFO> Stage Max-distance (nm)
INFO> 1 0.659
INFO> 2 0.627
INFO> 3 0.574
INFO> 4 0.528
INFO> 5 0.484
INFO> 6 0.447
INFO> 7 0.389
INFO> 8 0.346
INFO> 9 0.305
INFO> Step "cure_relax" initiated on 2 distances (max 0.305 nm)
INFO> Stage Max-distance (nm) Max-1-4-distance (nm)
INFO> 1 0.256 0.490
INFO> 2 0.208 0.447
INFO> 3 0.157 0.406
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.192 nm x 5.192 nm x 5.192 nm
INFO> Density 1057.63
INFO> Running-average-Density 1043.42
INFO> Rolling-10-average-Density 1056.08
INFO> Iteration 32 current conversion 0.950 or 380 bonds
With this conversion reached, now comes capping of the 20 oxirane rings that did not react:
INFO> ************************* Capping begins **************************
INFO> Capping will generate 20 new bonds
INFO> Step "cap_relax" initiated on 20 distances (max 0.252 nm)
INFO> Stage Max-distance (nm) Max-1-4-distance (nm)
INFO> 1 0.189 0.277
INFO> 2 0.174 0.281
INFO> 3 0.155 0.279
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.192 nm x 5.192 nm x 5.192 nm
INFO> Density 1057.48
INFO> Running-average-Density 1048.40
INFO> Rolling-10-average-Density 1058.75
INFO> ********** Connect-Update-Relax-Equilibrate (CURE) ends ***********
And finally, postcure equilibration and annealing:
INFO> *************** Postcure in proj-0/systems/postcure ***************
INFO> Annealing: 5 points for 2 cycles over 160 ps
INFO> Annealed coordinates in annealed.gro
INFO> Running Gromacs: npt ensemble; 100.00 ps, 300.00 K, 1.00 bar
INFO> Current box side lengths: 5.146 nm x 5.146 nm x 5.146 nm
INFO> Density 1085.93
INFO> Running-average-Density 1085.08
INFO> Rolling-10-average-Density 1087.24
INFO> *********** Final data to proj-0/systems/final-results ************
INFO> ********************* HTPolyNet runtime ends **********************
So we see our 95% cured system reached a density about 1.09 g/cc. I am not claiming any of these equilibration runs are long enough or the system is big enough, but this example just serves to illustrate how HTPolyNet works.
Let’s now take a look at some selected results.