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<div>you should go down the list and use all the tools, and use some from seperate software. In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian distribution, but it removes these. Somone e.lse here probably has better contributions though. It is hard to say without seeing the raw data though.</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 08. September 2014 um 10:25 Uhr<br/>
<b>Von:</b> "Ca C." <devila8@hotmail.com><br/>
<b>An:</b> "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se><br/>
<b>Betreff:</b> [gmx-users] g_mindist for hydrophobic interactions</div>
<div name="quoted-content">Dear All,<br/>
I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a "cross talk" for receptor's transactivation.<br/>
Is g_mindist a good tool for this purpose? Do you have more suggestions?<br/>
Moreover, should I use trjconv for pbc treatment before running g_mindist?<br/>
<br/>
Thank you in advance<br/>
<br/>
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