Hello, I performed molecular dynamics via gromacs on a biological system and now I would like to calculate electrostatic and van der waals interaction between two groups in my index file. However, it seems that it is impossible via gmx energy module and .edr file, since it does not prompt to select the group from index file. Can anyone help me with this?
thank you in advanced.
Arpit Jain
Use gmx mindist to calculate the minimum distance between the groups. Use gmx energy with a custom index file, specifying the groups for the interaction energy calculations: bashCopygmx energy -f ener.edr -n index.ndx Select the groups manually during the energy calculation prompt.
o calculate electrostatic and van der Waals interactions between two specific groups in GROMACS:
Alternatively, use gmx pairdist for more detailed pairwise interaction data.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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