[gmx-users] question about energygrps

[Hyunjin Kim]

>
>
> 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 that's outdated information.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
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
>