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

Subhashree Rout subhashree.rout at kiitbiotech.ac.in
Thu Feb 18 10:38:54 CET 2016


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
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
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

; 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
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

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