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

Mark Abraham 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 
> zero. 

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 
> 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

More information about the gromacs.org_gmx-users mailing list