Quoting Yoshiko Santoso <[EMAIL PROTECTED]>:
Dear Chris Neale,
Thank you very much for answering my questions in gmx-users mailing list.
(See Below)
> 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.
______________________________________________
I have another question, I hope you can help me.
I did the MD run with energy_excl, once the simulation is finished, where
can I obtain the total energy of the protein only?
What I put on mdp file is energy_excl = sol sol sol protein
Is it by looking at the md.log? but where is it exactly to look?
It is by g_energy (read the manual), but the value that is available
is not what I believe that you expect it to be and I think that you
may have missed the point of my suggestion. I think that you should
back up and tell us what you want to do and why and then we can offer
some better suggestions.
You will have better chance to get a reply by posting to the list.
Please post your reply under the same title as this email to the
mailing list.
Chris.
I'm fairly new with GROMACS, so I hope you can help me.
Thank you very much,
-Yoshiko-
Graduate Student
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