[gmx-users] Total energy of protein only

[chris.neale at utoronto.ca]

> Hi gmx-users,
>
> Can anyone tell me how to find the total energy of the protein only (not the
> system)?

You might try energygrp_excl SOL SOL
or energygrp_excl SOL SOL SOL PROTEIN
depending on what you want to acheive. THis will take care of all of  
the nonbonded interactions.

Without knowing what you want this value for, I can only warn you  
against trying to use this value as a measure of how "good" the  
structure is.

>
> What I've done is I minimized the system first, then I took out the water
> from the pdb file, then minimized it again without water, and get the total
> energy from the log file.

Why do a solvated minimization when you are then going to do a  
minimization in vaccuum?

> But when I'm comparing the result to get the delta Emm, the result did not
> make any sense.

Did not make sense how? We can't help without knowing what the problem is.

>
> Can someone help me on this please.
>
> Thank you very much,