[gmx-users] index file for interaction energies

Nick joojoojooon at gmail.com
Wed Feb 23 00:01:23 CET 2011 

One last question!

1- So what are the 12 energy terms I get by passing index file onto step 2
below?  I ignored rerun! what does rerun does?


2- So I dont have to include index file in mdrun initially..In brief what I
need is:


    step 1  grompp .....(no index)

    step 2  mdrun     -s old.tpr       -o old.trr       -c *.gro

(grompp and mdrun  as usual) then:

     grompp      -f energygroups.mdp         -c .top       -o new.tpr
    *-n index.ndx
*
        mdrun   *-s new.tpr      -rerun old.trr...*


Please confirm. Many thanks for your help.




On 22 February 2011 17:35, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
> --
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110222/31e0ea20/attachment.html>

More information about the gromacs.org_gmx-users mailing list