[gmx-users] Extract LJ-14 energy

[Justin Lemkul]

On 12/20/19 6:07 AM, Suvardhan Jonnalagadda wrote:
> Hi,
> Thanks for the reply.
> I have included it and rerun my system. Still problem prevails.

energrps are not required for LJ 1-4 energies, as these are 
intramolecular and energygrps correspond strictly to intermolecular 
interaction energies.

There is no need for enemat, which in any case is not practical to use 
enemat, just extract the energies with gmx energy. As Mark said, if your 
topology specifies 1-4 interactions, the energy contribution will be 
there. If it's not, there are no 1-4 interactions.

-Justin

>
>
> On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
> wrote:
>
>> Hi
>>     You have to mention energygrous in your .mdp file and rerun the
>> simulation. The details you'll get in gromacs protein- ligand complex
>> tutorial.
>>
>> On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, <
>> j.su.vardhan at gmail.com> wrote:
>>
>>> Hi All,
>>>
>>> *"GROMACS: VERSION 4.5.5; Precision: single"*
>>> I have performed an md simulation for 1 time step, on a single molecule
>>> with 17 atoms. I want to calculate all the energies (angle, dihedrals,
>>> bonds, 1-4 interactions), and compare. However, I am not able to get the
>>> LJ-14 interactions energy from the '*.edr'* file. When i searched in the
>>> manual, I came across *'gmx enemat'* command.
>>> I gave the following command
>>>
>>> *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'*
>>> In the groups.dat I have entered the molecule name (as in the *.itp
>>> *file).
>>>
>>> So, the error and warnings I get after the above command are as follows:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *"   group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in
>> energy
>>> fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy
>>> fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill
>>> select half-matrix of energies with 0 elementsLast energy frame read 0
>>> time    0.000            Will build energy half-matrix of 17 groups, 0
>>> elements, over 1 framesSegmentation fault (core dumped)   "*
>>> Is this a bug? or am I missing something?
>>> Also, what does 'LJ(SR)' term in the energies include? In my case, I have
>>> only one molecule. So, what does this LJ short range include?
>>>
>>> Thank you,
>>>
>>> Best regards,
>>> Vardhan
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
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