[gmx-users] question about energygrps

[Hyunjin Kim]

>
>
> 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
 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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