[gmx-users] index file for interaction energies

[Nick]

Dear Justin,

Thanks for your reply and Sorry for asking naive questions...

1- I am looking at all possible interaction energies between components A
and B. that is A-A AB and BB. So interaction between single chains is not
what I want. With this I think my initial approach was right. That is
putting all atoms of 3 A chains under [A] and the same all solvent atoms
under [B] and setting A and B as energy groups in mdp. Am I right?

2- One more thing bout question 3: I am passing on index.ndx to mdrun
command.

with the index file I talked about I am getting the follwoing for AA AB and
BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms).

I think you say I need rerun since you assumed I did not pass it onto mdrun.
right?

3- to get intermolecular interaction energies say for AA I need to add up LJ
SR+coulomb SR? say +123-50=73 ? or just take absolute values : 123+50=173 ?

Thanks,


>
> Nick wrote:
>
>> Dear experts,
>>
>> 1- I am trying to get interaction energies between solute (3 chains A) and
>> solvent 50 molecules B. In the index file I created two groups: one for all
>> atoms of [A] and and [B] for all solvent molecules. and by setting A and B
>> as energy groups in mdp file I am getting break down as A-A, A-B and B-B
>> with g_energy.
>>
>> I am a little confused as I dont know if I need to create different groups
>> for my solute to get interaction energies A-A, A-B and B-B. I mean do I need
>> to have [A1] for solute chain 1 ...[A3] for chain 3?
>>
>>
> If you want a breakdown of per-chain energetics, then yes, specify each
> chain as a group.  The programs will only do what you tell them, nothing
> more, nothing less.
>
>
>


>  and then sent A1, A2, A3 in mdp file and run g_energy? if I need to
>> specify different chains, then to get say A-A should I average over all
>> possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I am really confused ..
>>
>>
> Theoretically, the short-range terms should sum, not average.
>
>
>  2- I know it is naive question but What does A1-A1 mean? How can one chain
>> interact with itself?
>>
>>
> Without knowing what the chain is, no one can answer this.  Generally, any
> atoms that are within the short-range cutoff and further away than nrexcl
> bonds contribute to short-range interactions.  Long-range interactions
> (i.e., PME terms) happen too, but you can't decompose that term with
> energygrps.
>
>
>  3- Do I need to use mdrun - rerun option to get beakdown or just g_energy
>> gives what I need?
>>
>>
> You need to -rerun.  g_energy does not take an index file, and it only
> analyzes existing groups, it cannot derive new ones.
>
> -Justin
>
>
>  Thanks for your help
>> Paniz
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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