[gmx-users] grompp for minimization: note & warning

shahab shariati shahab.shariati at gmail.com
Sun Sep 15 09:44:21 CEST 2013

Dear gromacs users

My system contains 3 components: DOPC & cholesterol lipids + drug + water

In minimization step, when I use
grompp -f em.mdp -c system.gro -p topol.top -o em.tpr,
I encountered with following note and warning:

WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.200000)

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116
Estimate for the relative computational load of the PME mesh part: 0.62

NOTE 1 [file em.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


My em.mdp file is as follows:

; em.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
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

; Parameters describing how to find the neighbors of each atom
nstlist        = 1            ; Frequency to update the neighbor list and
long range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
rlist        = 1.2        ; Cut-off for making neighbor list (short range
coulombtype    = PME        ; Treatment of long range electrostatic
rcoulomb    = 1.2        ; Short-range electrostatic cut-off
rvdw        = 1.2        ; Short-range Van der Waals cut-off
pbc            = xyz         ; Periodic Boundary Conditions


I dont like to use -maxwarn option. How to modify parameters in em.mdp file
to resolve note an warning.

Any help will highly appreciated.

Best wishes.

More information about the gromacs.org_gmx-users mailing list