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

[Justin A. Lemkul]

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

========================================