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