[gmx-users] Re: Total Energy protein only

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Feb 8 19:31:32 CET 2008

Quoting Yoshiko Santoso <yoshiko.santoso at gmail.com>:

> 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.


> I'm fairly new with GROMACS, so I hope you can help me.
> Thank you very much,
> -Yoshiko-
> Graduate Student

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