Dataset Open Access

SIRAH-CoV2 initiative: S2 Spike core fragment in postfusion state (PDB id:6M1V)

Klein Florencia; Exequiel Barrera; Pablo Garay; Matías Machado; Martín Soñora; Sergio Pantano

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Spike S2 fragment in its postfusion form (PDB id: 6M1V). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020

The files 6M1V_SIRAHcg_rawdata_0-5us.tar, and 6M1V_SIRAHcg_rawdata_5-10us.tar, contain all the raw information required to visualize (on VMD 1.9.3), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at

Additionally, the file 6M1V_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6LU7_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.

To take a quick look at the trajectory:

1- Untar the file 6M1V_SIRAHcg_10us_prot_skip10ns.tar

2- Open the trajectory on VMD 1.9.3 using the command line:

vmd 6M1V_SIRAHcg_prot.prmtop 6M1V_SIRAHcg_prot.ncrst -e sirah_vmdtk.tcl

Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. 

This dataset is part of the SIRAH-CoV2 initiative.

For further details, please contact Florencia Klein ( or Sergio Pantano (

Files (18.5 GB)
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  • Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)

  • Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)

  • Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)

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