[gmx-users] RE:How to check for bad contacts.

[Lum Nforbi]

Hello Dr. Warren,

Thank you for the useful information.
I did use vmd to view my molecule, but in a system of 2000 molecules, it is
quite difficult to locate atom 2065 (an O atom) which is actually the
offending atom. I have described the way I did the work below. I used a
random generator software for starting coordinates. How do you reassign a
randomly generated coordinate?

The way I generated my initial coordinates for 2000 water is by first
drawing one molecule in ghemical, exported as a .pdb file, then used the
command below to add 2000 molecules of water to a box of dimensions 40 A
using a software for random coordinate generation called Packmol:

tolerance 2.0
output waters2000.pdb
filetype pdb
structure water.pdb
  number 2000
  inside cube 0. 0. 0. 40.
end structure

I then used editconf to change from .pdb to .gro since charmm27, which is
the forcefield I use, is not among the force fields displayed when I use the
pdb2gmx command.

editconf -f waters2000.pdb -o waters2000.gro

This editconf command reduces the previously defined box dimensions to zero.
So, I use this command to re-define the box dimensions and I don't know if
it is correct:

editconf -bt cubic -box 4.0 -f waters2000.gro -o waters2000d.gro

I then minimize the system via grompp and further minimize the system via
mdrun, then I get the error message that my system cannot be settled.

grompp -f waters_min.mdp -c waters2000d.gro -p water.top -o wmin_.tpr
mdrun -nice 0 -v -s wmin_.tpr -o wmin.trr -c waters2000d.gro -e
wmin_ener.edr

Output of minimization:
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =          500
Step=    0, Dmax= 1.0e-02 nm, Epot=  4.93923e+14 Fmax= 1.81064e+17, atom=
2035 Step=    1, Dmax= 1.0e-02 nm, Epot=  3.85283e+11 Fmax= 8.96443e+13,
atom= 2035
Step=    2, Dmax= 1.2e-02 nm, Epot=  2.83666e+09 Fmax= 4.79912e+11, atom=
2035
Step=    3, Dmax= 1.4e-02 nm, Epot=  5.92577e+07 Fmax= 7.02630e+09, atom=
2035
Step=    4, Dmax= 1.7e-02 nm, Epot=  5.71720e+06 Fmax= 2.14598e+08, atom=
793
Step=    5, Dmax= 2.1e-02 nm, Epot=  1.46839e+06 Fmax= 2.37662e+07, atom=
4936
Step=    6, Dmax= 2.5e-02 nm, Epot=  6.41000e+05 Fmax= 2.52111e+06, atom=
3232
Step=    7, Dmax= 3.0e-02 nm, Epot=  2.73384e+05 Fmax= 5.96696e+05, atom=
3688
Step=    8, Dmax= 3.6e-02 nm, Epot=  1.64413e+05 Fmax= 1.55972e+05, atom=
2686
Step=    9, Dmax= 4.3e-02 nm, Epot=  1.09639e+05 Fmax= 3.25690e+04, atom=
2389
Step=   10, Dmax= 5.2e-02 nm, Epot=  5.32635e+04 Fmax= 2.60651e+04, atom=
2065

t = 0.022 ps: Water molecule starting at atom 2065 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Thank you,
Lum
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