<div>eqs 19/20 were implemented for motion.</div><div>The problem was the calculation of com of a molecule splited across boundaries.with</div><div>calc_xcm that does not check for this.</div><div>Problem solved with suggestion of Mark.</div>
<div>Thanks</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Mon, Dec 14, 2009 at 8:04 AM, Omer Markovitch <span dir="ltr"><<a href="mailto:omermar@gmail.com">omermar@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div dir="ltr">See for example eq. 19 & 20 at JCP 129, 84505 (<a href="http://dx.doi.org/10.1063/1.2968608" target="_blank">http://dx.doi.org/10.1063/1.2968608</a>). Is this what you meant?<br>
<font color="#888888">Omer.</font><div class="im"><br><br><div class="gmail_quote">On Mon, Dec 14, 2009 at 06:56, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><div><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
I think that the problem comes from pbc handling for molecules splited across boundaries - I expect : do something before calc_xcm.<br>
I could run trjconv before run tool, but I 'd like to use the original trajectories and handle them correctly.<br>
Any suggestion is appreciable.<br>
</blockquote><br></div></blockquote></div><br></div></div>
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