[gmx-users] Fw: The results of your email commands

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 2 01:16:44 CET 2012

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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120102/cc78be0f/attachment.html>

More information about the gromacs.org_gmx-users mailing list