[gmx-users] question about energygrps

[Justin Lemkul]

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 that's outdated information.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

> 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
>>
>> ========================================
>> --
>> 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

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