[gmx-users] decomposing the energy

Mark Abraham Mark.Abraham at anu.edu.au
Sat May 14 14:42:36 CEST 2011

On 14/05/2011 9:11 PM, Justin A. Lemkul wrote:
> Ramachandran G wrote:
>> Hello gmx users:
>>       I did 1ns simulation for my system and have the trajectory and 
>> energy files.
>> Now i want to see the energy of some specific residues. So, i 
>> decompose(separated) the energy groups and edited the mdp file.
>> Using the mdp file, i created a new tpr file and rerun the mdrun 
>> using the trajectory file. But when i compared the total energy 
>> between the old and new one, it differs a lot.
>> I am doing some mistakes somewhere. Can anyone help me please. Thanks.
> Maybe, maybe not.  Without seeing the .mdp settings and the data that 
> you're looking at, all anyone can do is guess.  You also haven't 
> stated what type of trajectory (i.e. .xtc or .trr) you're using as 
> -rerun input.  If you're using an .xtc file, there is no velocity 
> information, so any property related to velocities (most notably 
> kinetic energy, but several others as well) will be zero.  I suspect 
> this is probably where the discrepancy is, but it is not a problem.  
> Using energygrps is only useful for decomposing short-range nonbonded 
> energy terms, nothing else.

Strictly speaking, one can decompose bonded energy terms too, with a 
well-constructed topology, but I agree with the rest of what Justin said.


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