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    On 1/01/2012 9:38 PM, banafsheh mehrazma wrote:
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        <div>Hi everyone,&nbsp;<br>
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                  <div>I am studying a paper about a DNA simulation
                    using Gromacs and &nbsp;I encountered this in ion
                    addition step:</div>
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                    <div>Na+ were added by replacing a solvent molecule
                      at ca. 6 &Aring;</div>
                    <div>from the phosphorus in the direction of the
                      bisector of the angle</div>
                    <div>&#8736;O1P-P-O2P (O1P and O2P being the phosphate
                      nonbridging</div>
                    <div>oxygen atoms)</div>
                    <div>I think what it means is that Na+ was added in
                      a distance of 6&nbsp;&Aring; from the phosphorus. How can we
                      specify this in GROMACS?</div>
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    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.<br>
    <br>
    Mark<br>
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