EMC, opls-ua toluene return wrong atom types

EMC
1

Hi, with the latest version I am not able correcly generate toluene molecule with OPLS-UA force field. Example toluene configuration in examples return correct 3d structure but only with #C4 united atoms types (see bellow). In previous version everything worked ok. I was some thread about missing rules with OPLS-AA force field and tried that approach but without success.

Would it be possible to shift back to previous version of EMC?

Thanks,
Martin Bures

***** toluene.data
LAMMPS output created by EMC v9.4.4, build Aug 8 2023 07:32:29

       7  atoms
       7  bonds
       8  angles
       8  dihedrals

       1  atom types
       1  bond types
       1  angle types
       1  dihedral types

         0    5.713127998  xlo xhi
         0    5.713127998  ylo yhi
         0    5.713127998  zlo zhi

Masses

   1   16.04260  # c4

Atoms

   1       1   1  0.0000   0.6501627730   0.5170452802   1.5800674300  # c4
   2       1   1  0.0000   0.1257001846  -0.7620728741   2.2413211116  # c4
   3       1   1  0.0000  -0.8259330069  -1.5186424446   1.2293514044  # c4
   4       1   1  0.0000  -2.1064414250  -2.2991633394   1.7329656045  # c4
   5       1   1  0.0000  -2.7495433991  -1.7085931109   3.1051832976  # c4
   6       1   1  0.0000  -1.6013281306  -1.4412575685   4.1443482324  # c4
   7       1   1  0.0000  -0.3738226608  -0.5274000264   3.7472043671  # c4

Bonds

   1       1       1       2  # c4,c4
   2       1       2       3  # c4,c4
   3       1       2       7  # c4,c4
   4       1       3       4  # c4,c4
   5       1       4       5  # c4,c4
   6       1       5       6  # c4,c4
   7       1       6       7  # c4,c4

Angles

   1       1       1       2       3  # c4,c4,c4
   2       1       1       2       7  # c4,c4,c4
   3       1       2       3       4  # c4,c4,c4
   4       1       2       7       6  # c4,c4,c4
   5       1       3       2       7  # c4,c4,c4
   6       1       3       4       5  # c4,c4,c4
   7       1       4       5       6  # c4,c4,c4
   8       1       5       6       7  # c4,c4,c4

Dihedrals

   1       1       1       2       3       4  # c4,c4,c4,c4
   2       1       1       2       7       6  # c4,c4,c4,c4
   3       1       2       3       4       5  # c4,c4,c4,c4
   4       1       2       7       6       5  # c4,c4,c4,c4
   5       1       3       2       7       6  # c4,c4,c4,c4
   6       1       3       4       5       6  # c4,c4,c4,c4
   7       1       4       3       2       7  # c4,c4,c4,c4
   8       1       4       5       6       7  # c4,c4,c4,c4
2

Hi Martin,

Deducing from the build timestamp, you used emc_linux_x86_64_v9.4.4_20230801.tgz. I typed toluene using the current emc_linux_x86_64_v9.4.4_20230801.tgz with

#!/usr/bin/env emc_setup.pl

ITEM	OPTIONS

replace		true
field		opls-ua
density		0.1
number		true
focus		true
emc_execute	true

ITEM	END

ITEM	SHORTHAND

molecule	c1ccccc1C,1

ITEM	END

and get the following in a .psf:

PSF NAMD CMAP

       2 !NTITLE
REMARK created by EMC v9.4.4, build Aug  8 2023 07:32:29
REMARK created on Mon Oct 23 07:12:38 2023

       7 !NATOM
       1 mole 1    mole C    cd                 0       13.0189       0
       2 mole 1    mole C1   cd                 0       13.0189       0
       3 mole 1    mole C2   cd                 0       13.0189       0
       4 mole 1    mole C3   cd                 0       13.0189       0
       5 mole 1    mole C4   cd                 0       13.0189       0
       6 mole 1    mole C5   ca                 0        12.011       0
       7 mole 1    mole C6   c32                0       15.0347       0

which are the types I would expect. I therefore cannot reconstruct your observation. For completeness sake, the LAMMPS data file also shows the same types:

LAMMPS output created by EMC v9.4.4, build Aug  8 2023 07:32:29

           7  atoms
           7  bonds
           8  angles
           8  dihedrals
           1  impropers

           3  atom types
           3  bond types
           4  angle types
           4  dihedral types
           1  improper types

             0    11.52301355  xlo xhi
             0    11.52301355  ylo yhi
             0    11.52301355  zlo zhi

Masses

       1   15.03470  # c32
       2   12.01100  # ca
       3   13.01890  # cd

Atoms

       1       1   3  0.0000   5.8702980380   4.5682829218   6.1069446572  # cd
       2       1   3  0.0000   5.3168387773   4.4060420645   4.7992128303  # cd
       3       1   3  0.0000   5.0392530385   5.5666403524   4.0919723244  # cd
       4       1   3  0.0000   5.1324096098   6.8852407785   4.6378052273  # cd
       5       1   3  0.0000   5.7335628072   7.0549325107   5.9236887027  # cd
       6       1   2  0.0000   6.0963570765   5.8610589722   6.6601220777  # ca
       7       1   1  0.0000   6.9792072104   5.9646093147   7.8560579759  # c32

Bonds

       1       2       6       1  # ca,cd
       2       3       1       2  # cd,cd
       3       3       2       3  # cd,cd
       4       3       3       4  # cd,cd
       5       3       4       5  # cd,cd
       6       2       6       5  # ca,cd
       7       1       7       6  # c32,ca

Angles

       1       3       1       6       5  # cd,ca,cd
       2       1       7       6       1  # c32,ca,cd
       3       4       1       2       3  # cd,cd,cd
       4       2       6       1       2  # ca,cd,cd
       5       4       2       3       4  # cd,cd,cd
       6       4       3       4       5  # cd,cd,cd
       7       2       6       5       4  # ca,cd,cd
       8       1       7       6       5  # c32,ca,cd

Dihedrals

       1       3       1       6       5       4  # cd,ca,cd,cd
       2       4       1       2       3       4  # cd,cd,cd,cd
       3       3       5       6       1       2  # cd,ca,cd,cd
       4       1       7       6       1       2  # c32,ca,cd,cd
       5       4       2       3       4       5  # cd,cd,cd,cd
       6       2       6       1       2       3  # ca,cd,cd,cd
       7       2       6       5       4       3  # ca,cd,cd,cd
       8       1       7       6       5       4  # c32,ca,cd,cd

Impropers

       1       1       6       7       1       5  # ca,c32,cd,cd

Can you share, what exactly you did? Have you tried installing a fresh version from online?

3

Dear Veld,

I was using the same configuration as you shared in text above. But for some strange reason, it did not worked.

I purged all EMC from system, downloaded fresh version and tried again. And it works as expected.

So, there must have been something wrong in my system, mayby some mix-up with older EMC version.

Sorry for trouble, now everything works fine.
Thanks a lot,
Martin Bures

4

Hi Martin,

Happy to help. Glad to hear things work as expected for you now.

Best,
Pieter