[gmx-users] CALCULATING ENERGY OF PROTEIN ONLY

[Mark Abraham]

radhika jaswal wrote:
> Hi all,
> 
> I want to calculate the energies of the protein or drug only not with 
> the water molecules. But edr files contain all the water md run data and 
> if I want to open n edit data, file doesn't gets open 'coz of the 
> character coding problem. If anybody has any solution to this problem 
> plz suggest as I want to compare the energies of the different 
> conformations of a single protein only.

You need to use the index groups feature - perhaps make_ndx and then 
g_energy -n. Certain groups, like "protein" and "solvent" can be 
implicitly created for you if your system is not too unusual, but for 
more elaborate needs, you should use make_ndx. Have a read of the 
relevant sections of the manual and g_energy -h and make_ndx -h.

Mark