Trappe force field error?

EMC
1

Hi Pieter,

Iā€™m trying to simulate C4 to C18 using Trappe. For capric acid for example, I get wrong number of atoms per molecule. Capric acid has 32 atoms per molecule. It worked fine for different force fields.

LAMMPS output created by EMC v9.4.4, build Feb 16 2025 06:45:02

    5681  atoms
    5244  bonds
    5244  angles
    4807  dihedrals
     437  impropers

       6  atom types
       6  bond types
       7  angle types
       7  dihedral types
       1  improper types

         0    51.78808599  xlo xhi
         0    51.78808599  ylo yhi
         0    51.78808599  zlo zhi

Masses

   1   12.01100  # c3oa
   2   14.02680  # c4h2
   3   15.03470  # c4h3
   4    1.00790  # ho
   5   15.99940  # o
   6   15.99940  # oha

Atoms

   1       1   3  0.0000  34.0160703272  36.2517950817  28.4093799995  # c4h3
   2       1   2  0.0000  32.8003491775  35.3875760233  28.4238127762  # c4h2
   3       1   2  0.0000  31.9218134310  35.3972141901  29.7583595571  # c4h2
   4       1   2  0.0000  30.4546024265  34.8822444187  29.5586727027  # c4h2
   5       1   2  0.0000  29.7360822198  34.2522930234  30.7886473262  # c4h2
   6       1   2  0.0000  28.3127596800  33.6788551381  30.4510875124  # c4h2
   7       1   2  0.0000  28.4364525291  32.7130206680  29.2607071044  # c4h2
   8       1   2  0.0000  27.1050109478  32.2380089870  28.7873762079  # c4h2
   9       1   2  0.0000  26.2027057232  33.4802067263  28.5509541337  # c4h2
  10       1   1  0.5400  24.7903530011  33.0005790309  28.3022119797  # c3oa
  11       1   5 -0.4500  24.4182201241  31.8545497217  28.3286880034  # o
  12       1   6 -0.4600  23.9075709801  34.1383536347  28.2813079457  # oha
  13       1   4  0.3700  23.0470462752  33.8127373075  28.2109192509  # ho
  14       2   3  0.0000  16.9030680887  29.7168698114  16.2418278485  # c4h3
  15       2   2  0.0000  16.4985767112  28.4577167606  15.5332982918  # c4h2
  16       2   2  0.0000  15.9962785997  27.2832512275  16.3983355314  # c4h2
  17       2   2  0.0000  14.5988284791  27.2932417827  16.8016247741  # c4h2
  18       2   2  0.0000  14.0025860756  25.9450603959  17.1972677485  # c4h2
  19       2   2  0.0000  13.5849144238  24.9717122756  16.0494756583  # c4h2
  20       2   2  0.0000  14.6196675335  24.7051416281  14.9346885874  # c4h2
  21       2   2  0.0000  13.9845852382  24.0539296883  13.7392532279  # c4h2
  22       2   2  0.0000  14.9001622100  24.1415283089  12.5032731237  # c4h2
  23       2   1  0.5400  14.3949469118  23.2033330339  11.3667759884  # c3oa
  24       2   5 -0.4500  14.8434508341  23.1646661257  10.2494929439  # o
  25       2   6 -0.4600  13.2900510172  22.4456632582  11.7399696454  # oha
  26       2   4  0.3700  12.9127773523  22.0059531136  10.9865854794  # ho

Here is the setup file

#!/usr/bin/env emc_setup.pl

Script: setup.esh

Author: EMC GUI v1.5.3, 23 July 2022

Date: Sun Jun 29 14:05:08 CEST 2025

Purpose: Input script for EMC Setup

Notes:

- Automatically generated by EMC GUI

- GUI developed by Marc Siggel, Eduard Schreiner, and Pieter J. in 't Veld

- Please include this reference in published work using EMC:

P.J in 't Veld and G.C. Rutledge, Macromolecules 2003, 36, 7358

Options section

ITEM OPTIONS

ncores 4
replace true
environment true

ITEM END # OPTIONS

Loops section

ITEM LOOPS

stage 00
trial 00

ITEM END # LOOPS

ITEM STAGE 00

Template section

ITEM TEMPLATE

Template options section

ITEM OPTIONS

density 0.90
field trappe
mol false
number true
pressure 1
profile density=false, pressure=false
sample energy=false, pressure=false, volume=false
temperature 320
replace true

ITEM END # OPTIONS

Groups section

ITEM GROUPS

capricacid CCCCCCCCCC(=O)O

ITEM END # GROUPS

Clusters section

ITEM CLUSTERS

@{CLUSTERS}

ITEM END # CLUSTERS

ITEM END # TEMPLATE

Trials sections

ITEM TRIAL 00

Clusters section

ITEM CLUSTERS

capricacid capricacid 437

ITEM END # CLUSTERS

Best regards,
Yunes Salman

2

Hi Yunes,

I think that you are not realizing, that ā€“ when using field trappe ā€“ EMC Setup will default to trappe-ua, i.e. the united atom variety of TraPPE. United atom force fields typically fold hydrogens into the bead representing the carbon they are connected to, thus using an implicit rather than an explicit representation. The types as listed in your LAMMPS data file mean

  • c3oa: a carbon with three connections connected to an acidic oxygen
  • c4h2: a carbon with four connection with two incorporated hydrogens
  • c4h3: a methyl carbon with three incorporated hydrogens
  • ho: a hydrogen connected to an oxygen
  • o: a double-bonded oxygen
  • oha: an oxygen connected to a hydrogen in a carboxylate

It is typical for united atom force fields to have an explicit representation for hydrogens connected to oxygens or nitrogens, since they tend to have partial charges associated with them. In total, 19 hydrogens are implicitly represented by the carbons they are connected to. Adding this to the 13 displayed beads per molecule makes a total of 32 atoms, not all of which are explicitly represented.

As an aside: the benefit of united atom force fields ā€“ as opposed to all atom force fields ā€“ is the lower number of atoms combined with a reduced number of non-zero partial charges. This results in a more speedy simulation.

1 Like
3

Hi Pieter,

Thank you very much for the detailed explanation!

Best regards,
Yunes Salman