On 5/3/13 11:27 AM, Ewaru wrote:
Hi,
Just wondering. My system shows this: "System has non-zero total charge:
11.999998"
and thus, I use the command as below to add 12 Cl to the protein:
"genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn
12"
However, when I checked the genion.log file, it shows that the system has
total charge of 12. Isn't it supposed to be 0? This is what the genion.log
shows:
The charge that genion reports is the one that it finds in the system contained
in the .tpr file. grompp reports a net charge of 12 (or close enough to it, see
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) and genion
confirms that is what it finds. The next invocation of grompp will confirm that
your net charge is zero.
-Justin
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Using shifted Lennard-Jones, switch between 0 and 1 nm
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: 12.000
Generated table with 1200 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for LJ12Shift.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC-like water optimization for 3745014 molecules.
Thank you.
Best regards,
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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