<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">Thanks MARK for your reply,and your suggestion is very helpful.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">I don't write back until mdrun ends just now.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">I want to simulate DMSO property as it is cooled. So I put 500 DMSO moleculers in a box. Ref_t =300<span style="mso-spacerun: yes"> </span>ref_P=1.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">During the first 60ps ,the 500 DMSO moleculers seems to be diffusing outside with box getting larger and larger.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">Then box size become stable until 290ps from when box get smaller and smaller, DMSO meoleculers form several clusters. Gradually clusters get bigger and bigger ,at last there are three big moleculer blocks in box with two relatively smaller blocks.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">During 1000 -1300ps,big moleculer continue gathering and form two main blocks ,one is in the upside of the box ,and another is in the underside of the box. This two blocks' size keep changing ,but the number of blocks never changed . the whole simulating system has already been stable when 1500ps comes.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">300 K temperature and 1 bar pressure means DMSO is in liquid phase. So I think DMSO moleculers shoud gather and form relatively big blocks. But I expect there is only one block in box,and simulation results give two blocks .</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">By the way, I have searched many DMSO literaures ,but never seen information about c-c bond and c-o bonds in gmx force field . maybe I am quite new ,and not good at English .</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">Thanks MARK again for your suggestion and kindness.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">Your sincerely</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Calibri">Kelvin wang </font></span></p><br><br>
<div><span class="gmail_quote">2008/5/22, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div><span class="e" id="q_11a0f8685e35ea5a_0">wang kelvin wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi, everyone.<br><br>I am simulating DMSO. At fisrst ,bond parameters contain two c-c bonds,and c-o bond ,which actually not in existence. But gmx 's force field ffg53a6 documents in top directory defines these bonds. When running mdrun , system reminds "segmentation default". then i get these virtual bond away , since that mdrun is ok !<br>
<br>Can anyone tell me why gmx define these bonds (ie. C-O bond ,C-C bond)? And has eliminating these bonds effects on simulating result?<br><br> <br>Any suggestion is appreciated.<br></blockquote><br></span></div>I'd suggest describing your observations more coherently and in more detail.<br>
<br>Otherwise, with a view to using SHAKE, some united-atom DMSO models prefer to define six bonded interactions, rather than three bonded interactions and three angle interactions. Thus, DMSO C-C and C-O interactions can exist. However, you should already know about this from reading the literature about your DMSO model, right? :-)<br>
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