[gmx-users] energy minimization

ikjk 1761440083 at qq.com
Tue Sep 25 10:48:03 CEST 2018

   I am doing a md with martini force filed,I create a box, there is a double monolayer, then I solvate it, but when I did energy minimization, 	 	 	 	 
gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr          then

NOTE 1 [file minim.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 562058480
Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'DPPC'
Excluding 1 bonded neighbours molecule type 'W'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 72143      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 261042.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118
 	 	 	 	Estimate for the relative computational load of the PME mesh part: 0.91

NOTE 2 [file minim.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.


gmx mdrun -v -deffnm em

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=   14, Dmax= 1.2e-06 nm, Epot=  2.36880e+22 Fmax=         inf, atom= 2016
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.

writing lowest energy coordinates.
it just stopped with 14 steps, here is my mdp file,if you can solve this problem, I will appreciate that.

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep         ; Algorithm (steep = steepest descent minimization)
emtol       = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01          ; Minimization 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    ; Buffered neighbor searching
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 in all 3 dimensions


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