<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">Thanks for reply</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">RMSD means root mean square deviation.</font></span></p>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">I am researching DMSO properties during phase changes from nomal temperature to low tempreture. </font></span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">At first step,I want to produce fully equilibrant systems at different temperature. Of course ,there are many important parameters computed ,which can be used to judge whether stable state reaches . </font></span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">But RMSD's curve is relatively smooth , and covenient to see .So I take it as most important parameter to judge equilibrium. Only when RMSD plot level, i do other computation and see whether they reach equilibrium too. </font></span></div>
<div class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman"></font></span> </div>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">Your sincerly</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman">wang</font></span></p><br><br>
<div><span class="gmail_quote">2008/8/5, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">why RMSD?<br><br>On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel<br><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>
> wang kelvin wrote:<br>>><br>>> hi:<br>>> i am doing simulation of a system consists of 512 DMSO moleculers and<br>>> 917 water moleculers.<br>>> the whole system is running under 290K and 1bar ,and constraints = none;<br>
>> the simulation has taken 8000 ps ,but it seems not to get stable<br>>> yet,because RMSD keeps rising.<br>>> when i did simulation of the same system with constraints set all-bonds,it<br>>> usually get stable within 3000ps.<br>
>> i wonder whether any mistakes has been made or it is normal.<br>>> can you give some hints?<br>>> thanks.<br>><br>> what rmsd?<br>><br>>><br>>><br>>> ------------------------------------------------------------------------<br>
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> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>
> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface<br>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>
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</blockquote></div><br>