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

shahab shariati shahab.shariati at gmail.com
Mon Sep 16 09:06:55 CEST 2013

Dear Justin

Very thanks for your reply.

You said "I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check". I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for my case.

Based on your suggestion, I used -maxwarn option for grompp. Then I used
-nt 1 option for mdrun,
but this step takes too long and

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
********************   This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 23: Water molecule starting at atom 10613 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 2122 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.4310875e+05
Maximum force     =  2.7179752e+04 on atom 5271
Norm of force     =  4.0253470e+02
my em.mdp file is as follows:

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
gro, edr, trr and lof file were created.

I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp
file, but result are the same.

Is this minimization completely true?
Can I use created gro file of this minimization for next step

I am beginner in gromacs, please help me to resolve this problem.

Best wishes

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