Thanks Tsjerk and Mark!<br><br>After setting the box I measured the distance of the last protein <br>atom and the box edge it was not same all the sides. Any comments on this?<br><br>I have sent another question regarding minimization but no replys yet.<br>
Kindly reply Sir!<br><br>Thanking you<br>MKS <br> <br><br><br><div class="gmail_quote">On Fri, Jan 14, 2011 at 10:42 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br><br><span>On 01/14/11, <b>Kavyashree M </b> <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>Thank you Tsjerk for your suggestions!</div></blockquote><br></div>Please leave old email context in so that people can find out what you are talking about. Only to you is your email so important that you might remember all the details :-)<br>
<br><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div><div class="im">So according to this my minimal box size should be <br>0.6nm in order to avoid PBS effects and due to the <br>
water effects i have to set it 1nm or higher.<br><br></div><div class="im">So this rule is irrespective of the box type we choose<br>
isnt it?<br></div></div></blockquote><br>1) You need a minimum amount of water between solutes to have a reasonably physical model.<br>2) You wish to minimize the cost of that water by the choice of box shape and size.<br>
<font color="#888888"><div><br>Mark<br>
</div>
</font><br>--<br>
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