[gmx-users] calculating energy between certain groups

Irem Altan irem.altan at duke.edu
Tue May 15 21:26:33 CEST 2018


I ran a simulation using GPUs, and now I would like to calculate the energy between two protein chains, as well as energy between the protein and the solvent. For this, I am trying to run enemat:

gmx enemat -f umbrella0.edr

but this fails:

Opened umbrella0.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
WARNING! could not find group Coul-SR:Protein-SOL (0,1)in energy file
WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file

I read here (https://redmine.gromacs.org/issues/1822) that this information is not written into the .edr files when the simulation is run on GPUs. I am using version 2016.3, but there are some simulation results with 5.1.2 that I would like to analyze as well. Is it true that this is not possible with my setup? If so, is there a workaround like calculating energies given individual snapshots, rather than having to deal with .edr files?


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