On 1/01/2012 9:38 PM, banafsheh mehrazma wrote:
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?
You'll need to find one manually. Set up some index groups and use them
with g_dist to measure distances. Or whatever else floats your boat.
Mark
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