[gmx-users] energy minimization - infinite force on atom

Evelyne Deplazes 20400454 at student.uwa.edu.au
Thu Apr 8 08:23:36 CEST 2010

Hi gmx-users

I am somehow famliar with gromacs but only used it with coarse grained force
fields (Martini) so far, not with all atom ones. I am now trying to run a
simulation on a membrane protein system (protein embedded in a POPC bilayer
solvated with water) using the gromos force field (Gromacs 4.0.2  ffG53a).
Using gromacs tutorials I managed to create the required input files (.gro,
.top and .itp). I at at the stage of running a energy minimization using
position restraints on the protein and the peptide molecules. I can grompp
the input files

grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx

with the following input file:

define          = -DPOSRES -DPOSRES_LIPID
integrator      = steep         ; Algorithm (steep = steepest descent
emtol           = 100.0         ; 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 and how to
calculate the interactions
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 forces)
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 (yes/no)

and the following topology file

; Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include chain topologies
#include "protein.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_protein.itp"

; Include POPC topology
#include "popc.itp"

#include "lipid_posre.itp"

; Include water topology
#include "spc.itp"

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
mscl protein with POPC bilayer

[ molecules ]
; Compound        #mols
Protein             1
POPC                242
SOL                 32145
CL-                 91
NA+                 91

When I run the simulation I get the following output after 16 steps of the
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.

Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  8.0175742e+17
Maximum force     =            inf on atom 4443
Norm of force     =            inf

It seems there is an infinite force on atom 4443 but I don't really
understand what that means. The confout.gro structure looks ok ie the system
has not "exploded". Should the protein not be restrained? How do I know my
position restraints actually work? I tried increasing the force constant of
the restraints or removing the restraints but still get the same output. I
also tried adding -DFLEXIBLE since I am using the spc model, but still the
same output.

can anyone tell me what that message actually means and what is wrong with
my system?


Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
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