Project ID: plumID:21.025
Name: Computational and biochemical analysis of type IV pilus dynamics and stability
Archive: https://zenodo.org/record/4903970/files/T4P_MD_PLUMED.zip
Category: bio
Keywords: molecular dynamics, calcium binding, Type IV pilus
PLUMED version: 2.6
Contributor: Yasaman Karami
Submitted on: 07 Jun 2021
Publication: Y. Karami et al., Computational and biochemical analysis of type IV Pilus dynamics and stability, (2021)

PLUMED input files

File Compatible with
MU_Ions/T4P_C118C130S_HSE_calcium/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_C50C60S_HSE_calcium/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_E5A_HSE/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_E5A_HSE_calcium/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_WT_HSE_calcium_150mM/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_WT_HSE_magnesium_100mM/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_WT_HSE_manganese_100mM/plumed.dat tested on v2.7 tested on master
MU_Ions/T4P_WT_HSE_sodium_100mM/plumed.dat tested on v2.7 tested on master
WT/T4P_WT_HSD_calcium/plumed.dat tested on v2.7 tested on master
WT/T4P_WT_HSE/plumed.dat tested on v2.7 tested on master
WT/T4P_WT_HSE_calcium/plumed.dat tested on v2.7 tested on master
WT/T4P_WT_HSP_calcium/plumed.dat tested on v2.7 tested on master
WT_temp/T4P_WT_HSE_60deg/plumed.dat tested on v2.7 tested on master
WT_temp/T4P_WT_HSE_80deg/plumed.dat tested on v2.7 tested on master
WT_temp/T4P_WT_HSE_calcium_60deg/plumed.dat tested on v2.7 tested on master
WT_temp/T4P_WT_HSE_calcium_80deg/plumed.dat tested on v2.7 tested on master

Last tested: 14 Jun 2021, 15:47:06

Project description and instructions
All the input files (topology, setup, plumed files) for the MD simulations of the wild-type EHEC Type 4 Pilus studied in different conditions, i.e., in presence and absence of different ions, protonation states, and salt concentrations, as well as point mutations, are deposited here. The simulations were carried out using GROMACS 2019.4 package and PLUMED 2.6.0.

Submission history
[v1] 07 Jun 2021: original submission

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plumeDnest:21.025