[gmx-users] problem with energy groups and mdrun -rerun option
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 21 23:37:09 CEST 2010
jagannath mondal wrote:
> Justin,
> Thanks for your reply. Then I wonder whether there is any other way
> out in gromacs to get the net interaction potential energy due to each
> of the components in a simulations.
>
> I am asking this, many times people report the potential energy
> contribution due to solvent-solvent interaction in a simulation
> containing solute( say peptide) and solvents and that are also being
> done in gromacs. I wonder, for those cases, whether just adding the
> non-bonding interaction will be good enough ? or, there is any other way
> out ?
Solvent-solvent interactions should describe just the nonbonded part of the
potential, assuming they're referring to intermolecular interactions. As it
stands, these are the only interactions that can be decomposed in Gromacs
without seriously overhauling the code.
-Justin
> Jagannath
>
> --- On *Fri, 22/10/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun
> option
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Friday, 22 October, 2010, 2:56 AM
>
>
>
> jagannath mondal wrote:
> > Hi,
> > I have used gromacs 4.0.7 to do MD simulation of two solutes
> A & B in water ( solvent) . Initially, I had set "energy groups =
> system " and used mdrun to do the simulation.
> >
> > Now,I wanted to get the potential energy contribution from due to
> interaction of A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.
> > For that I followed some discussions in mailing list regarding
> using mdrun -rerun option:
> > This is what I did:
> > I used make_ndx and created 3 groups: A, B and solvent. Now, I
> modified the grompp.mdp file so that I have now energy groups = A
> B solvent
> > Then I used grompp -c conf -f grompp -n index -o topol
> >
> > Then I used mdrun -s -rerun traj_old.xtc
> > ( here traj_old.xtc is the old xtc file I obtained during the
> original mdrun)
> >
> > But, now, after using this -rerun option , if I try to use the
> g_energy on the resulting ener.edr file to obtain the individual
> potential energy of interaction for A-A, B-B , A-B, A-solvent
> > I get following output
> >
> > Here is the output from g_energy -f ener.edr :
> >
> > Select the terms you want from the following list by
> > selecting either (part of) the name or the number or a combination.
> > End your selection with an empty line or a zero.
> > -------------------------------------------------------------------
> > 1 Bond 2 Angle 3 U-B 4
> Ryckaert-Bell.
> > 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8
> LJ-(SR) 9 Coulomb-(SR) 10 Coul.-recip. 11
> Potential 12 Kinetic-En. 13 Total-Energy 14
> Conserved-En. 15 Temperature 16 Pressure-(bar)
> > 17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY 20
> Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ
> 24 Vir-ZX 25 Vir-ZY 26 Vir-ZZ 27
> Pres-XX-(bar) 28 Pres-XY-(bar) 29 Pres-XZ-(bar) 30
> Pres-YX-(bar) 31 Pres-YY-(bar) 32 Pres-YZ-(bar) 33
> Pres-ZX-(bar) 34 Pres-ZY-(bar) 35 Pres-ZZ-(bar) 36
> #Surf*SurfTen 37 Mu-X 38 Mu-Y 39 Mu-Z
> 40 Coul-SR:A-A 41 LJ-SR:A-A 42 Coul-14:A-A 43
> LJ-14:A-A 44 Coul-SR:A-B 45 LJ-SR:A-B
> 46 Coul-14:A-B 47 LJ-14:A-B
> 48 Coul-SR:A-Solvent 49
> LJ-SR:A-Solvent 50 Coul-14:A-Solvent
> 51 LJ-14:A-Solvent 52 Coul-SR:B-B
> 53 LJ-SR:B-B 54
> Coul-14:B-B 55 LJ-14:B-B
> 56 Coul-SR:B-Solvent 57 LJ-SR:B-Solvent
> 58 Coul-14:B-Solvent 59
> LJ-14:B-Solvent 60 Coul-SR:Solvent-Solvent
> 61 LJ-SR:Solvent-Solvent 62
> Coul-14:Solvent-Solvent 63 LJ-14:Solvent-Solvent
> 64 T-System 65 Xi-System
> >
> > It provides me contribution from each of the energy groups on
> nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) . But, it
> does NOT provide me their contribution to Bonding term( i.e
> bond,angle, U-B,RB,improper-Dih) !! As a result, I am a not sure
> how to get the net potential energy from each of the 3 energy
> groups. Am I doing something wrong ? Do I need to use any other
> utilities ?
>
> Using energygrps only allows you to decompose nonbonded
> interactions. You cannot decompose bonded interactions, potential,
> kinetic energy, etc.
>
> -Justin
>
> > Any help will be useful.
> > Jagannath
> >
> >
>
> -- ========================================
>
> 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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--
========================================
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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