Hi everyone,
I am studying a paper about a DNA simulation using Gromacs and I encountered
this in ion addition step:
Na+ were added by replacing a solvent molecule at ca. 6 Å
from the phosphorus in the direction of the bisector of the angle
∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging
oxygen atoms)
I think what it means is that Na+ was added in a distance of 6 Å from the
phosphorus. How can we specify this in GROMACS?
there is no such option in genion tool in gromacs package.
Thank you
B.Mehrazma
--- Begin Message ---
Hi everyone,
I am studying a paper about a DNA simulation using Gromacs and I encountered
this in ion addition step:
Na+ were added by replacing a solvent molecule at ca. 6 Å
from the phosphorus in the direction of the bisector of the angle
∠O1P-P-O2P (O1P and O2P being the phosphate nonbridging
oxygen atoms)
I think what it means is that Na+ was added in a distance of 6 Å from the
phosphorus. How can we specify this in GROMACS?
there is no such option in genion tool in gromacs package.
Thank you
B.Mehrazma
--- End Message ---
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