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 /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun
option
To: "Discussion list for GROMACS users" <gmx-users@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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