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?
By using a text editor, or finding a different method for generating the
coordinates. It is not terribly difficult to parse out the relevant molecules
in VMD, by using "resid" or "index" specifiers. See the VMD manual.
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
This should be fine; I don't know if you might also need to use the -c flag to
center the system in the box.
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.
You don't minimize with grompp, only mdrun :)
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
The magnitude of the potential and the forces indicates that there should be
some very obvious atomic overlap in the starting structure. Visual inspection
in VMD (see above) should show you what's going on.
The other option that I can think of to build a suitable system is simply to
make use of genbox and the built-in, pre-equilibrated water boxes that are
distributed with Gromacs.
-Justin
Thank you,
Lum
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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