[gmx-users] problem with energy groups and mdrun -rerun option

jagannath mondal jmondal2004 at yahoo.co.in
Thu Oct 21 23:34:55 CEST 2010

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 ?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.


>  Any help will be useful. 
> Jagannath

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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