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

[Mark Abraham]

Hi,

There's something catastrophically wrong with your input structure. Look it
with a visualization program, e.g. VMD, PyMol

Mark

On Thu, Feb 18, 2016 at 10:39 AM Subhashree Rout <
subhashree.rout at kiitbiotech.ac.in> wrote:

> 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
> --
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