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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