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

banafsheh mehrazma bmehrazma at yahoo.com
Sun Jan 1 11:38:41 CET 2012

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120101/8c6adcf1/attachment.html>
-------------- next part --------------
An embedded message was scrubbed...
From: banafsheh mehrazma <bmehrazma at yahoo.com>
Subject: a question about ion addition
Date: Sun, 1 Jan 2012 02:23:29 -0800 (PST)
Size: 4972
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120101/8c6adcf1/attachment.mht>

More information about the gromacs.org_gmx-users mailing list