Hello:
I've got a question on energygrps options in .mdp file. This option is
usually used for establishing the groups for the energy output. I am
going to study the entropy changes of protein-ligand-SOL in a membrane
system, I am just wondering shall I specify each compoenent in
energygrps option, like:
energygrps = Protein LIG SOL POPC
I am also going to use g_lie for interaction analysis, will the above
options be sufficient?
If I forgot to assign the energygrps options in my md.mdp file during MD
simulations, is it any fast way to calculate the energy after MD instead
of running the simulation from beginning?
I notice that there is a tool called g_lie can be used to evaluate
protein/ligand binding, I am just wondering is there any paper on this
tool? I don't find too much informations on gromacs manual.
thank you very much
Albert
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