[gmx-users] question about energygrps

[Hyunjin Kim]

>
>
> 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.

>
> -Justin
>
>>   13  Temperature     14  Pres.-DC        15  Pressure        16  Box-X
>>   17  Box-Y           18  Box-Z           19  Volume          20
>> Density
>>   21  pV              22  Enthalpy        23  Vir-XX          24  Vir-XY
>>   25  Vir-XZ          26  Vir-YX          27  Vir-YY          28  Vir-YZ
>>   29  Vir-ZX          30  Vir-ZY          31  Vir-ZZ          32
>> Pres-XX
>>   33  Pres-XY         34  Pres-XZ         35  Pres-YX         36
>> Pres-YY
>>   37  Pres-YZ         38  Pres-ZX         39  Pres-ZY         40
>> Pres-ZZ
>>   41  #Surf*SurfTen   42  Box-Vel-XX      43  Box-Vel-YY      44
>> Box-Vel-ZZ
>>   45  T-System
>>
>>
>>
>>
>>
>>>>
>>>>>
>>>>>> In log file, "energygrp-flags[  0]: 0".
>>>>>> I think this means it calculate system energies instead of two
>>>>>> specific
>>>>>> groups I choose.
>>>>>>
>>>>>
>>>>> Some energy terms are decomposable, most are not.  There will be
>>>>> obvious
>>>>> differences in group names in the g_energy output.
>>>>>
>>>>
>>>> I thought nonbonded energy terms were supposed to be decomposable,
>>>> since
>>>> the two groups I selected are from one in solute and one in solvent.
>>>> Am
>>>> I
>>>> wrong?
>>>>
>>>
>>> You will only get decomposed terms in the context of the interactions
>>> of
>>> those
>>> residues.  Again, seeing the full g_energy selection menu would help us
>>> in
>>> solving your problem.  Thus far, I can see no evidence that Gromacs has
>>> done
>>> anything wrong, but I also haven't seen any diagnostic evidence of what
>>> you have
>>> tried to do.  Please provide the details I have requested.
>>>
>>> -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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