[gmx-users] error in running md

[Mark Abraham]

Hi,

Technically this is energy minimization, not md. But likely the energy
should be negative. It's hard to help because you haven't told us what is
in the system, but if it's multiple organic molecules, start with one, to
see if your topology works appropriately.

Mark

On Tue, 13 Jun 2017 12:45 VARSHA RANI <varsha24_sps at jnu.ac.in> wrote:

> Hi,
>
> I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
> minimization is positive.
>
> *here is th screen output*
>
> Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
> 3521
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.1#
>
> Steepest Descents converged to Fmax < 10 in 4510 steps
> Potential Energy  =  4.0655389e+02
> Maximum force     =  9.8620596e+00 on atom 352
> Norm of force     =  3.3500545e+00
>
> NOTE: 16 % of the run time was spent in pair search,
>       you might want to increase nstlist (this has no effect on accuracy)
>
>
> *Below is txt of minim.mdp file *
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator    = steep        ; Algorithm (steep = steepest descent
> minimization)
> emstep          = 0.01         ; Energy step size
> ;emtol        = 1000.0      ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> nsteps        = 500000     ; Maximum number of (minimization) steps to
> perform
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist            = 10              ; Frequency to update the neighbor
> list and long range forces
> rlist            = 2         ; cut-off for making neighbour list (short
> range forces)
> cutoff-scheme       = Verlet
> ns_type            = grid        ; Method to determine neighbor list
> (simple, grid)
> coulombtype        = PME        ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 0.9         ; Short-range electrostatic cut-off
> rvdw            = 0.9        ; Short-range Van der Waals cut-off
> pbc            = xyz         ; Periodic Boundary Conditions (yes/no)
>
>
>
> regards
> --
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