[gmx-users] potential energy

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 18 21:30:39 CEST 2009

rams rams wrote:
> Hi,
> I run a regular MD on a peptide with several conformations. I want to 
> estimate the potential energy of each conformer. When I try using 
> "g_energy" with the option of "Potential" using the corresponding ".edr" 
> file, I am getting the average potential energy. But I am thinking that 
> it is the average potential energy of the system rather than the peptide 
> alone (correct me if I am wrong). There is no option with "g_energy" to 
> use an index file. Also I am not sure is there any way I can create the 
> ".edr" file for the peptide alone ? 
> Also let me know in case any other command would do the trick ?

You need to have created an index file with groups that interest you and 
supplied it to grompp with an .mdp file that uses them to do either the 
initial simulation, or a rerun. Check out the manual for help on groups, 
energy groups and the relevant .mdp file options. If your system is 
simply peptide+water, then you can use the default Protein group as an 
energy group.

Whether said average energies will tell you anything is quite another 
matter. :-)


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