[gmx-users] error in running md

[Vytautas Rakeviius]

Check structure, mainly atom numbers given in messages. Bad contacts or something.
 

    On Tuesday, June 13, 2017 1:45 PM, 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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