[gmx-users] decomposing the energy

[Sikandar Mashayak]

Hey Mark

Do you mean removing all bond definitions from topology file, when you say
well constructed topology to exclude all bonded-interactions in rerun?

thanks
sikandar

On Sat, May 14, 2011 at 8:01 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
>
> Mark
>
>
>
>> 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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>>
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