[gmx-users] RE:How to check for bad contacts.
Mark.Abraham at anu.edu.au
Fri Nov 20 14:17:46 CET 2009
Lum Nforbi wrote:
> 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
This is likely to generate a random starting structure, and that will
require care and attention to minimize and equilibrate. GROMACS provides
genbox to do this for you, and leave you with a starting structure that
already has physically reasonable water coordinates, which is much
preferable. Use genbox.
> 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
Probably there was no box information in waters2000.pdb, so none in
>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
> 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,
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