[gmx-users] question about energygrps

[Justin Lemkul]

On 5/12/13 1:31 PM, Hyunjin Kim wrote:
>>
>>
>> On 5/12/13 1:14 PM, Hyunjin Kim wrote:
>>>>
>>>>
>>>> On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>>>>>>
>>>>>>
>>>>>> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
>>>>>>> Dear,
>>>>>>>
>>>>>>> I want to calculate LJ and Electrostatic energies between two groups
>>>>>>> defined in index.ndx during rerun with original trajectory.
>>>>>>>
>>>>>>> The following is what I tried:
>>>>>>>
>>>>>>> 1. insert "energygrps r_1 r_25" in the test.mdp file.
>>>>>>>
>>>>>>> 2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx
>>>>>>>
>>>>>>> 3. mdrun -nt 2 -rerun o.trr -s x.tpr -o x.trr -c x.gro -g x.log -e
>>>>>>> x.ene
>>>>>>>
>>>>>>> The simulation runs properly, but if I collect energy using
>>>>>>> g_energy,
>>>>>>> then
>>>>>>> values of all energy terms are same, although I choose different
>>>>>>> groups.
>>>>>>
>>>>>> Which specific groups did you choose?
>>>>>
>>>>> Thanks a lot. I chose residues 1 and 25.
>>>>>
>>>>
>>>> I understood that from the original post.  What I was asking about was
>>>> the
>>>> exact
>>>> groups you chose from the g_energy selection menu.
>>>>
>>>
>>> When I use g_energy, I chose 4 5 6 7 8 9 10 from the below list. Thanks.
>>>
>>>     1  Bond             2  Angle            3  Ryckaert-Bell.   4  LJ-14
>>>     5  Coulomb-14       6  LJ-(SR)          7  Disper.-corr.    8
>>> Coulomb-(SR)
>>>     9  Coul.-recip.    10  Potential       11  Kinetic-En.     12
>>> Total-Energy
>>
>> Dispersion correct, PME mesh (Coul-recip), and total potential are not
>> decomposable.  The other terms you selected should be.  The fact the these
>> options do not appear in the .edr file indicate either (1) you did not
>> rerun
>> with the right .tpr file or (2) you analyzed the wrong .edr file.  The
>> approach
>> you have suggested is correct and should result in the desired energy
>> groups
>> being present.  What version of Gromacs are you using?
>
> I use 4.6.1 with gpu.
>

Are you doing the rerun on GPU, as well, or on CPU?  What happens if you run in 
serial (-nt 1)?  I don't believe reruns work properly in parallel, but maybe 
that's outdated information.  Does a rerun on the .xtc file produce the desired 
output?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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