[gmx-users] Error running simulations with the protein frozen

Nuo Wang wolich22 at gmail.com
Sat Mar 26 02:43:24 CET 2016

Hi Gromacs admins,

I am trying to run MD simulations of protein solvated in water. I want to
completely freeze the protein at its crystal conformation and only sample
the solvent degrees of freedom (for comparison with Poisson-Boltzmann
calculations that only use the crystal structure). I tried to follow the
typical minimization-equilibration-production procedure described here:

But I get this error at the energy minimization step:
"Fatal error:
step 11: Water molecule starting at atom 60322 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate."

If I take away the freeze protein commands in my minimize.mdp, then no
error occurs:
freezegrps    = Protein
freezedim     = Y Y Y

I checked my atom 60322, it is next to the protein, but it is neither
clashing with anyone nor moving rapidly in my trajectory. Reducing timestep
by 1000 times won't help either, error just occurs at a later step.

I wonder how can I resolve this problem?
The script that I used is shown here, the input files in the script are
linked below:
### Generate topology
echo 9  | gmx pdb2gmx -f complex.pdb -o complex.gro -p complex.top -merge
all -ignh -water tip3p
### Generate box information
          gmx editconf -f complex.gro -o complex_newbox.gro -bt cubic -c
-box 11 11 11
### Add water
          gmx solvate -cp complex_newbox.gro -cs spc216.gro -o
complex_solvated.gro -p complex.top
### Prepare ion parameters
          gmx grompp -f ions.mdp -c complex_solvated.gro -p complex.top -o
### Add ions
echo 13 | gmx genion -s ions.tpr -o complex_solvated_ions.gro -p
complex.top -pname NA -nname CL -neutral -conc 0
### Generate index file
echo q  | gmx make_ndx -f complex_solvated_ions.gro -o index.ndx
### Preparation for energy minimization for the non-protein atoms
          gmx grompp -f minimize.mdp -c complex_solvated_ions.gro -n
index.ndx -p complex.top -o em.tpr
### Energy minimization for the non-protein atoms
          gmx mdrun -v -deffnm em -nt 1


Thanks a lot!

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