[gmx-users] question about energygrps

[Justin Lemkul]

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?

-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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>

-- 
========================================

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

========================================