Skip to content

Iermi peg paper #1698

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
iermi wants to merge 19 commits into
base: master
Choose a base branch
from
Open

Iermi peg paper #1698

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
33708bb
the molecule of di-propylene glycol methylene ether
iermi Jun 30, 2026
94cc8a0
one di-propylene glycol methylene ether, pdb-structure
iermi Jun 30, 2026
38a85b3
PGME.pdb renamed
iermi Jun 30, 2026
3513904
Renamed PGME.py
iermi Jun 30, 2026
9f21ca9
PGME and 30 wt % of water
iermi Jul 1, 2026
532bc29
PGME and 40 wt % of water
iermi Jul 1, 2026
3c6a29f
Add files via upload
iermi Jul 1, 2026
a07c90f
PGME and 50 wt % of water
iermi Jul 1, 2026
4eae971
PGME and 60 wt % of water
iermi Jul 1, 2026
4e045a5
pdb-files and a structural file from Gromacs
iermi Oct 4, 2026
c5557e4
Create README.md for PEG paper file descriptions
iermi Oct 4, 2026
7c5ae34
Fix typo in README example description
iermi Oct 4, 2026
3df0ff0
Fix formatting of example file name in README
iermi Oct 4, 2026
6134140
Fix formatting of code snippet in README.md
iermi Oct 4, 2026
1d4fa07
convert the system from Gromacs to OpenMM
iermi Oct 11, 2026
7df12a4
Files which were used in conversion from Gromacs
iermi Oct 11, 2026
6147446
Create forcefield.itp for OPLS-AA force field
iermi Oct 11, 2026
9b5c798
Folder contains files from OPLSAA force field
iermi Oct 11, 2026
dc22631
files for simulating in open mm
iermi Oct 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
240 changes: 240 additions & 0 deletions examples/PEG_PAPER/GROMACS/PGM.itp
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,240 @@
;
; File 'topol.top' was generated
; By user: inna (1000)
; On host: inna-ThinkPad-T14-Gen-5
; At date: Sun Sep 6 20:48:21 2026
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2022.6 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /home/inna/MDMC_TESTS_PEG/sim1
; Command line:
; gmx pdb2gmx -f PGME.pdb -o PGME.gro
; Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
;#include "./forcefield.ff/forcefield.itp"

[ moleculetype ]
; Name nrexcl
PGM 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 PGM rtp PGM q 0.0
1 opls_181 1 PGM C1 1 0.25 12.011
2 opls_180 1 PGM O1 2 -0.65 15.9994
3 opls_182 1 PGM C2 3 0.2 12.011
4 opls_183 1 PGM C3 4 0 12.011
5 opls_181 1 PGM C4 5 0.24 12.011
6 opls_180 1 PGM O2 6 -0.65 15.9994
7 opls_182 1 PGM C5 7 0.2 12.011
8 opls_183 1 PGM C6 8 0.23 12.011
9 opls_181 1 PGM C7 9 0.23 12.011
10 opls_154 1 PGM O3 10 -0.8 15.9994
11 opls_156 1 PGM H1 11 0.03 1.008
12 opls_156 1 PGM H2 12 0.03 1.008
13 opls_156 1 PGM H3 13 0.03 1.008
14 opls_156 1 PGM H4 14 0 1.008
15 opls_156 1 PGM H5 15 0 1.008
16 opls_156 1 PGM H6 16 0.04 1.008
17 opls_156 1 PGM H7 17 0.03 1.008
18 opls_156 1 PGM H8 18 0.03 1.008
19 opls_156 1 PGM H9 19 0.03 1.008
20 opls_156 1 PGM H10 20 0 1.008
21 opls_156 1 PGM H11 21 0 1.008
22 opls_156 1 PGM H12 22 0.04 1.008
23 opls_156 1 PGM H13 23 0.03 1.008
24 opls_156 1 PGM H14 24 0.03 1.008
25 opls_156 1 PGM H15 25 0.03 1.008
26 opls_155 1 PGM H16 26 0.4 1.008 ; qtot 0

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 11 1
1 12 1
1 13 1
2 3 1
3 4 1
3 14 1
3 15 1
4 5 1
4 6 1
4 16 1
5 17 1
5 18 1
5 19 1
6 7 1
7 8 1
7 20 1
7 21 1
8 9 1
8 10 1
8 22 1
9 23 1
9 24 1
9 25 1
10 26 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 14 1
1 15 1
2 5 1
2 6 1
2 16 1
3 7 1
3 11 1
3 12 1
3 13 1
3 17 1
3 18 1
3 19 1
4 8 1
4 20 1
4 21 1
5 7 1
5 14 1
5 15 1
6 9 1
6 10 1
6 14 1
6 15 1
6 17 1
6 18 1
6 19 1
6 22 1
7 16 1
7 23 1
7 24 1
7 25 1
7 26 1
9 20 1
9 21 1
9 26 1
10 20 1
10 21 1
10 23 1
10 24 1
10 25 1
14 16 1
15 16 1
16 17 1
16 18 1
16 19 1
20 22 1
21 22 1
22 23 1
22 24 1
22 25 1
22 26 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 11 1
2 1 12 1
2 1 13 1
11 1 12 1
11 1 13 1
12 1 13 1
1 2 3 1
2 3 4 1
2 3 14 1
2 3 15 1
4 3 14 1
4 3 15 1
14 3 15 1
3 4 5 1
3 4 6 1
3 4 16 1
5 4 6 1
5 4 16 1
6 4 16 1
4 5 17 1
4 5 18 1
4 5 19 1
17 5 18 1
17 5 19 1
18 5 19 1
4 6 7 1
6 7 8 1
6 7 20 1
6 7 21 1
8 7 20 1
8 7 21 1
20 7 21 1
7 8 9 1
7 8 10 1
7 8 22 1
9 8 10 1
9 8 22 1
10 8 22 1
8 9 23 1
8 9 24 1
8 9 25 1
23 9 24 1
23 9 25 1
24 9 25 1
8 10 26 1

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
11 1 2 3 3
12 1 2 3 3
13 1 2 3 3
1 2 3 4 3
1 2 3 14 3
1 2 3 15 3
2 3 4 5 3
2 3 4 6 3
2 3 4 16 3
14 3 4 5 3
14 3 4 6 3
14 3 4 16 3
15 3 4 5 3
15 3 4 6 3
15 3 4 16 3
3 4 5 17 3
3 4 5 18 3
3 4 5 19 3
6 4 5 17 3
6 4 5 18 3
6 4 5 19 3
16 4 5 17 3
16 4 5 18 3
16 4 5 19 3
3 4 6 7 3
5 4 6 7 3
16 4 6 7 3
4 6 7 8 3
4 6 7 20 3
4 6 7 21 3
6 7 8 9 3
6 7 8 10 3
6 7 8 22 3
20 7 8 9 3
20 7 8 10 3
20 7 8 22 3
21 7 8 9 3
21 7 8 10 3
21 7 8 22 3
7 8 9 23 3
7 8 9 24 3
7 8 9 25 3
10 8 9 23 3
10 8 9 24 3
10 8 9 25 3
22 8 9 23 3
22 8 9 24 3
22 8 9 25 3
7 8 10 26 3
9 8 10 26 3
22 8 10 26 3

69 changes: 69 additions & 0 deletions examples/PEG_PAPER/GROMACS/convert_from_gromacs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
import parmed as pmd
import openmm as mm
from openmm import app, unit

# Input files
topology_file = "topol.top"
coordinates_file = "pgme_280K_50W_125_1028.pdb"

# Read the complete GROMACS topology and coordinates.
# The topology must include the correct force-field files.
structure = pmd.load_file(
topology_file,
xyz=coordinates_file
)

# Report topology counts.
print("Atoms:", len(structure.atoms))
print("Residues:", len(structure.residues))
print("Bonds:", len(structure.bonds))
print("Angles:", len(structure.angles))
print("Periodic dihedrals:", len(structure.dihedrals))
print("RB torsions:", len(structure.rb_torsions))

# Check for missing coordinates.
if any(atom.xx is None or atom.xy is None or atom.xz is None
for atom in structure.atoms):
raise ValueError("Some atoms are missing coordinates.")

# Check periodic box information.
print("Box:", structure.box)

if structure.box is None:
raise ValueError(
"No periodic box was found. Check the PDB CRYST1 record "
"and the original GROMACS box information."
)

# Construct the OpenMM system.
# IMPORTANT: adjust these settings to match your original npt.mdp.
system = structure.createSystem(
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * unit.nanometer,
constraints=app.HBonds,
rigidWater=True,
removeCMMotion=False
)

# Save the OpenMM System.
with open("system.xml", "w") as f:
f.write(mm.XmlSerializer.serialize(system))

# Save the coordinates and topology in OpenMM-compatible formats.
with open("system.pdb", "w") as f:
app.PDBFile.writeFile(
structure.topology,
structure.positions,
f,
keepIds=True
)

print("\nOpenMM system saved to system.xml")
print("Particles:", system.getNumParticles())

print("\nOpenMM forces:")
for force in system.getForces():
print(type(force).__name__)

if isinstance(force, mm.RBTorsionForce):
print(" RB torsions:", force.getNumTorsions())
Loading
Loading