[gmx-users] index file for interaction energies

[Justin A. Lemkul]

Nick wrote:
> 
> 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?
> 

If you don't want your energies on a per-chain basis, then yes.

> 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?
> 

You need to create a new .tpr file that has the desired groups specified in it. 
  You pass the new .tpr file to mdrun, in conjunction with your old trajectory 
(i.e., mdrun -s new.tpr -rerun old.trr).

> 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 ?
> 

Sign matters a lot.  Positive is repulsive, negative is attractive.  You can't 
just switch them arbitrarily.

-Justin

> 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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto: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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

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

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

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