[gmx-users] Potential energy of protein after energy minimization

[Subhashree Rout]

Hii

I am simulating protein (PfCDPK5) in water. After performing energy
minimization, the potential energy of my protein is 2.86082e+07. As
mentioned in the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html,
the Epot should be negative.

The em.mdp file-
; minim.mdp - used as input into grompp to generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist            = 1            ; Frequency to update the neighbor list
and long range forces
cutoff-scheme   = Verlet
ns_type            = grid        ; Method to determine neighbor list
(simple, grid)
coulombtype        = PME        ; Treatment of long range electrostatic
interactions
rcoulomb        = 1.0        ; Short-range electrostatic cut-off
rvdw            = 1.0        ; Short-range Van der Waals cut-off
pbc                = xyz         ; Periodic Boundary Conditions (yes/no)

Kindly suggest where I am going wrong.

-- 
Subhashree Rout
PhD Scholar
Bioinformatics Lab
KIIT School of Biotechnology
KIIT University
Bhubaneswar
Odisha
INDIA
Pin-751024