Skip to main content

Table 1 Example of analysis input and output files

From: Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS

Input files

Gromacs package analysis

Output 1

Output 2

2mu8_sd_em.edr

Energy

2mu8_potentialsd.xvg

2mu8_potentialsd.png

2mu8_cg_em.edr

Energy

2mu8_potentialcg.xvg

2mu8_potentialcg.png

2mu8_nvt.edr

Energy

2mu8_temperature_nvt.xvg

2mu8_temperature_nvt.png

2mu8_npt.edr

Energy

2mu8_temperature_npt.xvg

2mu8_temperature_npt.png

2mu8_em.tpr and 2mu8.xtc

rms

2mu8_rmsd_cris.xvg

2mu8_rmsd_cris.png

2mu8_pr.tpr and 2mu8.xtc

rms

2mu8_rmsd_prod.xvg

2mu8_rmsd_prod.png

2mu8_pr.tpr and 2mu8.xtc

gyrate

2mu8_gyrate.xvg

2mu8_gyrate.png

2mu8_pr.tpr and 2mu8.xtc

rmsf

2mu8_rmsf_residue.xvg

2mu8_rmsf_residue.png

2mu8_pr.tpr and 2mu8.xtc

sasa

2mu8_sas_residue.xvg

2mu8_sas_residue.png

  1. Input files are generated after executing an ‘mdrun’ command and depend on each specific step. Output 1 and 2 files will be made available in the zipped file for download. Output 2 refers to files generated after running application ‘grace’ or ‘xmgrace’ over.xvg files as instructed in the Gromacs manual. In this example, the input and output files refer to a protein contained in the 2mu8.pdb file uploaded in the initial screen.