[gmx-users] minimization is not converging

[Bratin Kumar Das]

Dear all,
             I am running a membrane simulation with GCGR protein. I am
getting the following warning and error

gmx mdrun -v -s em_1.tpr -deffnm em_1
                      :-) GROMACS - gmx mdrun, 2016.5 (-:

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GROMACS:      gmx mdrun, version 2016.5
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/workstation/Documents/GROMACS_projects/GROMACS_GCGR_new
Command line:
  gmx mdrun -v -s em_1.tpr -deffnm em_1


Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256

  Hardware topology: Basic

Reading file em_1.tpr, VERSION 2016.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =         2000

WARNING: Listed nonbonded interaction between particles 19562 and 19566
at distance 2.420 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



WARNING: Listed nonbonded interaction between particles 9914 and 9918
at distance 2.232 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



WARNING: Listed nonbonded interaction between particles 29342 and 29348
at distance 2.250 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Step=    0, Dmax= 1.0e-02 nm, Epot=  1.42935e+20 Fmax=         inf, atom=
15058
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.42929e+20 Fmax=         inf, atom=
15058
Step=   15, Dmax= 1.5e-06 nm, Epot=  1.42941e+20 Fmax=         inf, atom=
15058
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (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.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 10.
Potential Energy  =  1.4292894e+20
Maximum force     =            inf on atom 15058
Norm of force     =            inf

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