[gmx-users] decomposing the energy

Mark Abraham Mark.Abraham at anu.edu.au
Sat May 14 15:01:02 CEST 2011

On 14/05/2011 10:52 PM, XAvier Periole wrote:
> 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 
> file.

Reruns do neighbour searching every frame, regardless.


> 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
>> MILES-IGERT Trainee
>> 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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