[gmx-users] decomposing the energy

XAvier Periole x.periole at rug.nl
Sat May 14 14:52:33 CEST 2011

Two things you have to be careful about:
1- use trr trajectory files. xtc precision is not sufficient and it  
will give a lot of discrepancies at least for the bonded terms.
2- set the nstlist to 1 as the neiboring list should be undated for  
each frame and not every 5/10 as it is normally set in a regular mdp  

On May 14, 2011, at 1:11 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.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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