[gmx-users] index file for interaction energies
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 23 00:07:48 CET 2011
Nick wrote:
> 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?
>
>
I don't know what 12 terms you're referring to. You'll get A-A, A-B, and B-B
short-range nonbonded terms, the exact enumeration of which will depend on the
settings in your .mdp file.
The -rerun function is explained in the manual, or alternatively "mdrun -h." I
assumed (perhaps incorrectly) that you had generated a trajectory using some
energygrps and you wished to make changes after the fact in the way the
nonbonded potential was decomposed.
> 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.
>
You don't necessarily need the -rerun function if you plan ahead. Using mdrun
-rerun is only useful in the case that you haven't set your energygrps properly
and you don't want to completely run the simulation over again.
-Justin
>
>
>
> On 22 February 2011 17:35, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> 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
>
> ========================================
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--
========================================
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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