Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations" (doi:10.18419/darus-3313)

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Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"

doi:10.18419/darus-3313

DaRUS

2023-03-13

1

Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2023, "Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"", https://doi.org/10.18419/darus-3313, DaRUS, V1

Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"

doi:10.18419/darus-3313

Gravelle, Simon (Universität Stuttgart)

Beyer, David (Universität Stuttgart)

Brito, Mariano E. (Universität Stuttgart)

Schlaich, Alexander (Universität Stuttgart)

Holm, Christian (Universität Stuttgart)

268449726

429529433

327154368 - SFB 1313

397384169 - FOR2811

EXC 2075 - 390740016

DaRUS

Gravelle, Simon

Huber, Frank

Gravelle, Simon

2022-12-20

https://doi.org/10.18419/darus-3313

Chemistry, Physics, Molecular Dynamics Simulation, GROMACS, ESPResSo

Simulations and data analysis scripts for the publication "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations". The dataset contains two types of simulation scripts: all-atom simulation (GROMACS) and coarse-grained simulations (ESPRESSO). In both cases, the system is a polymer PEG bulk system. See the <a href="https://darus.uni-stuttgart.de/file.xhtml?fileId=180668">README file</a> for details and instructions.

Simon Gravelle, David Beyer, Mariano Brito, Alexander Schlaich, Christian Holm: Reconstruction of NMR Relaxation Rates from Coarse-Grained Polymer Simulations, ChemRxiv, 2022. Preprint.

10.26434/chemrxiv-2022-f90tv-v2

Simon Gravelle, David Beyer, Mariano Brito, Alexander Schlaich, Christian Holm: Reconstruction of NMR Relaxation Rates from Coarse-Grained Polymer Simulations, ChemRxiv, 2022. Preprint.

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README.md

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Instruction for using this repository

text/markdown

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analysis_NMRforMD.py

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Python script to analysis NMR relaxation time

text/x-python

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buildall.sh

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Bash script to create GROMACS system

application/x-sh

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simulation_PEG_H2O_all_atom.sh

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Bash script to execute NMR measurement in GROMACS

application/x-sh

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tip4peps.itp

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GROMACS force field file

application/vnd.shana.informed.formtemplate

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viscosity_PEG_H2O_all_atom.sh

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Bash script to execute viscosity measurement in GROMACS

application/x-sh

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waterPEGmixture.ipynb

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Jupyter notebook to create a PEG mixturre

application/x-ipynb+json

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atomtypes.atp

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GROMACS force field file

application/octet-stream

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ffbonded.itp

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GROMACS force field file

application/vnd.shana.informed.formtemplate

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ffnonbonded.itp

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GROMACS force field file

application/vnd.shana.informed.formtemplate

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forcefield.itp

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GROMACS force field file

application/vnd.shana.informed.formtemplate

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peg.itp

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GROMACS force field file

application/vnd.shana.informed.formtemplate

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em.mdp

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GROMACS input file

application/octet-stream

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npt.mdp

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GROMACS input file

application/octet-stream

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npt1000.mdp

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GROMACS input file

application/octet-stream

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nvt.mdp

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GROMACS input file

application/octet-stream

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run.mdp

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GROMACS input file

application/octet-stream

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visco.mdp

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GROMACS input file

application/octet-stream

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charmm.file

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GROMACS force field file

application/octet-stream

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endpatch.dat

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GROMACS force field file

text/x-fixed-field

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monomer.dat

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GROMACS force field file

text/x-fixed-field

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analysis_NMRforMD.py

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Python script for NMR calculation from Espresso trajectory

text/x-python

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analyze_data_angular_potential.py

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Python script for angular potential analysis

text/x-python

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input_parameters.txt

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Input parameters for Espresso simulations

text/plain

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merge_traj_file_angular_potential.sh

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Bash script to merge trajectory

application/x-sh

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run_with_condor_coarse_grained.sh

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Bash file to run Espresso simulations on condor

application/x-sh

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simulate_peg_coarse_grained.py

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Python script for Espresso simulations

text/x-python

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run_with_condor_coarse_grained_viscosity_angular_potential.sh

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Bash file to run Espresso simulations

application/x-sh

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simulate_peg_coarse_grained_viscosity_measurements_angular_potential.py

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Python script for Espresso calculation of viscosity

text/x-python