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

[Evelyne Deplazes]

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
minimization)
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
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
ns_type         = grid          ; Method to determine neighbor list (simple,
grid)
rlist           = 1.2           ; Cut-off for making neighbor list (short
range forces)
coulombtype     = PME           ; Treatment of long range electrostatic
interactions
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"
#endif

; Include POPC topology
#include "popc.itp"

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

; 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
minimisation
-------------------------------------------------------------------------------------------------------------------
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?

thanks


-- 
Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
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