[gmx-users] energy_terms

[balaji nagarajan]

Dear Users 

I have a peptide, (1AKI.pdb)

My aim is to solvate it in the presence of the explicit water molecules
and do minimization and to split the energy terms , and to see the energy contribution from each terms 

for this i have done the following in gromacs 

-----------------------------------------------------------------------------------
pdb2gmx -ignh -ff gromos43a1 -f 1AKI.pdb -o 1AKI_processed.gro -water spc
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
------------------------------------------------------------------------------------

the minim.mdp file is as follows 

---------------------------------------------------
define               = -DFLEXIBLE
constraints          = none
integrator           = cg
dt                   = 0.001     ; ps !
nsteps               = 1000
nstlist              = 10
ns_type              = grid
rlist                = 1.0
coulombtype          = PME
rcoulomb             = 1.0
vdwtype              = cut-off
rvdw                 = 1.0
optimize_fft         = yes
;
;        Energy minimizing stuff
;
emtol                = 10.0
emstep               = 0.01

energygrps = protein SOL
------------------------------------------------

in the above i have given the energy groups, protein and solvent 

after minimization one can get the energy values from all the possible contributions as follows

g_energy -f em.edr

in this term it is not possible to separate the bond distance and the bond angle term for the protein and water separately, 

How to get these terms separately for water and the protein for this minimized structure ? ( for a single structure)

I can not under stand the earlier explanation , could any one can tell in detail 

thanks in advance 








 		 	   		  
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