[gmx-users] EM error

[Xu Dong Huang]

Dear users,

Now I fixed the initial structure error, and I solvated it in water (martini bead model), and i run typical EM, I get the following error: 

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        50000
Step=   14, Dmax= 1.2e-06 nm, Epot=  4.48322e+19 Fmax=         inf, atom= 14524
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =  4.4832208e+19
Maximum force     =            inf on atom 14524
Norm of force     =            inf

gcq#182: "That Was Cool" (Beavis and Butthead)

-----My EM.mdp file contains the following: 
integrator               = steep
dt                       = 0.020
nsteps                   = 50000 ;Note: 100 steps is to much for a vacuum run (nsteps=10)

nstlog                   = 1000
nstenergy                = 500
nstxtcout                = 500

nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
periodic_molecules       = no
rlist                    = 1.4

coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15
epsilon_rf               = 1
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                     = 1.2

My system size 73191 W, and 1 star (consisted of 101 atoms)
I read somewhere that it's that atom 14524 is overlapping… I can't visually see anything complicated in my VMD since the system is pretty big 

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu