[gmx-users] energy_terms

[Justin A. Lemkul]

balaji nagarajan wrote:
> 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
> 

Bonded terms cannot be decomposed for systems composed of different types of 
molecules.  I believe what was suggested was to use tpbconv and trjconv to 
create trajectories with subsets of the system (for instance, the protein alone) 
which can be processed with mdrun -rerun to recalculate bonded interactions, 
which will now correspond to only the molecule(s) present.

Use of rigid water (standard) or constraints on bonds (also typical) removes 
some bonded terms in favor of constraint RMSD terms.

-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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