<div>Hello Dr. Warren,</div>
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<div>Thank you for the useful information.</div>
<div>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?</div>
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<div>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:<br>
<br>tolerance 2.0<br>output waters2000.pdb<br>filetype pdb<br>structure water.pdb<br> number 2000<br> inside cube 0. 0. 0. 40.<br>end structure <br><br>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. <br>
<br>editconf -f waters2000.pdb -o waters2000.gro<br><br>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:<br>
<br>editconf -bt cubic -box 4.0 -f waters2000.gro -o waters2000d.gro<br><br>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. <br>
<br>grompp -f waters_min.mdp -c waters2000d.gro -p water.top -o wmin_.tpr<br>mdrun -nice 0 -v -s wmin_.tpr -o wmin.trr -c waters2000d.gro -e wmin_ener.edr<br><br><span style="TEXT-DECORATION: underline">Output of minimization</span>:<br>
Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 500<br>Step= 0, <span class="yshortcuts" id="lw_1258721067_1">Dmax</span>= 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<br>
Step= 2, Dmax= 1.2e-02 nm, Epot= 2.83666e+09 Fmax= 4.79912e+11, atom= 2035<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 5.92577e+07 Fmax= 7.02630e+09, atom= 2035<br>Step= 4, Dmax= 1.7e-02 nm, Epot= 5.71720e+06 Fmax= 2.14598e+08, atom= 793<br>
Step= 5, Dmax= 2.1e-02 nm, Epot= 1.46839e+06 Fmax= 2.37662e+07, atom= 4936<br>Step= 6, Dmax= 2.5e-02 nm, Epot= 6.41000e+05 Fmax= 2.52111e+06, atom= 3232<br>Step= 7, Dmax= 3.0e-02 nm, Epot= 2.73384e+05 Fmax= 5.96696e+05, atom= 3688<br>
Step= 8, Dmax= 3.6e-02 nm, Epot= 1.64413e+05 Fmax= 1.55972e+05, atom= 2686<br>Step= 9, Dmax= 4.3e-02 nm, Epot= 1.09639e+05 Fmax= 3.25690e+04, atom= 2389<br>Step= 10, Dmax= 5.2e-02 nm, Epot= 5.32635e+04 Fmax= 2.60651e+04, atom= 2065<br>
<br>t = 0.022 ps: <span class="yshortcuts" id="lw_1258721067_2" style="CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed">Water molecule</span> starting at atom 2065 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>
Wrote <span class="yshortcuts" id="lw_1258721067_3" style="CURSOR: hand; BORDER-BOTTOM: #0066cc 1px dashed">pdb files</span> with previous and current coordinates</div>
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<div>Thank you,</div>
<div>Lum<br></div>