[gmx-users] a question on energygrps

Albert mailmd2011 at gmail.com
Sun Jul 14 12:21:40 CEST 2013


  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

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