Ni hao Xi Zhao,<br><br>Please note again that you're working with projections. There is not necessarily a single conformation that corresponds to the energy minimum from your projection space. <br>You can obtain the minimum from the 2D projection and then find the conformation that yields the projection closest to that point, by taking the Euclidean distance between the projection and the minimum. You'll have to do a bit of scripting there.<br>
<br>Cheers,<br><br><br>Tsjerk<br><br><div class="gmail_quote">On Mon, Dec 21, 2009 at 2:51 PM, xi zhao <span dir="ltr"><<a href="mailto:zhaoxiitc2002@yahoo.com.cn">zhaoxiitc2002@yahoo.com.cn</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;">
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<div>Dear Mr <b>Tsjerk Wassenaar ：</b></div>
<div><b>Thank you for your help! </b></div>
<div><b>what you said is reasonal, but how to </b>implement them, or detial procedure? The 2d projections can convert to a free energy landscape, and how to obtain conformation in the minimum of energy surface?</div>
<div>best regards! <br><br><br><a href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel="nofollow" target="_blank"><img src="" alt="4" border="0"></a><br>
<br>--- <b>09年12月21日，周一, Tsjerk Wassenaar <i><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></i></b> 写道：<br></div>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"><br>发件人: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>><br>主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection<br>
收件人: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>日期: 2009年12月21日,周一,下午7:57<div><div></div><div class="h5"><br><br>
<div>Ni hao,<br><br>Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the time for which the point corresponds with the one your interested in, and extract the conformation from the trajectory.<br>
<br>Cheers,<br><br>Tsjerk<br><br>
<div class="gmail_quote">2009/12/20 xi zhao <span dir="ltr"><<a href="http://cn.mc151.mail.yahoo.com/mc/compose?to=zhaoxiitc2002@yahoo.com.cn" rel="nofollow" target="_blank">zhaoxiitc2002@yahoo.com.cn</a>></span><br>
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<td style="font-family: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">Dear users for gromacs:<br>We know that observing the sampled conformations in the subspace spanned<br>by the eigenvectors is a so-called two-dimensional projection(2D<br>
projection), in 2-D projection, each point represents a snapshot from<br>the simulation, and the distribution shows the sampled region along the<br>first two eigenvectors during the simulation. But I feel confounded,<br>because I do not know to how to obtain corresponding conformation for<br>
each point in the 2-D projection.Please help me!<br>best regards!<br>thank you!<br><br><br><a href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel="nofollow" target="_blank"><img src="" alt="4" border="0"></a></td>
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<br>Computational Chemist<br>Medicinal Chemist<br>Neuropharmacologist<br><br></div><br></div></div>-----下面为附件内容-----<br><br>
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<br>Computational Chemist<br>Medicinal Chemist<br>Neuropharmacologist<br><br>