<br><br><div class="gmail_quote">2009/7/20 Vitaly V. Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="gmail_quote"><div>Hi Matteus,<br><br>Yeah, dynamic groups would be a powerfull tool. But such mechanism is still under development if I am not out-of-time.<br><br>The possible way to proceed with such kind of research (as Berk advised me here long ago) is to sort the trajectory (trjorder) based on the distance criteria. Then you can make an index file with N first numbers (which are close to the protein) and use g_energy with this group and protein group. It seems for your task this way is a perfect solution.</div>
</div></blockquote><div><br>Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use g_energy? This way you would be free of any problems with molecules going in and out of your solvation shell, if I am getting things right.<br>
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