[gmx-users] question about energygrps

[Hyunjin Kim]

>
>
> On 5/12/13 1:53 PM, Hyunjin Kim wrote:
>>>
>>>
>>> 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?
>>>
>>
>> I am about test on rerun with -nt 1 or CPU. But, previously, I only
>> tested
>> rerun with -nt 2 and GPU and looked to produce proper output. However,
>> what you mean "desired output" seems nonbonded interactions between two
>
> The proper output is an .edr file with the decomposed energy terms you
> want, so
> I don't understand what "looked to produce proper output" means.  Any
> other
> output (trajectory, coordinate, log, etc) should be identical to the
> previous
> run, since you're doing a rerun, not a new simulation.
>
> -Justin

I see. Then no I have not obtained the proper result yet. I will test what
you suggested.
Thanks. Hyunjin.

>
>> groups I set, which I have not. I will test rerun in CPU and even -nt 1
>> and see whether I got results properly.
>> Thanks a lot for your support.
>>
>> Hyunjin.
>>
>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> 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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>>
>>
>
> --
> ========================================
>
> 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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