<br /><br /><span>On 01/10/11, <b class="name">yuanyuan wang </b> <yilin3201@126.com> wrote:</span><blockquote cite="mid:78c95ae3.a721.12d6f17eace.Coremail.yilin3201@126.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div>sorry to say I can not found a center for the trj. I tried to make bigger box by trjconv -box -boxcenter, but it seems that the trj only exist in the old box area ,bigger box cannot stop jumps.</div>
<div>Is it really happened that I can do nothing with it ? </div></div></blockquote><br />No. Justin gave you a good suggestion. What happened when you tried it?<br /><br />Mark<br /><br /><blockquote cite="mid:78c95ae3.a721.12d6f17eace.Coremail.yilin3201@126.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div ><br/></div>
<div> yuanyuan wang</div>
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<div>Message: 1<br />Date: Fri, 7 Jan 2011 02:56:08 -0800<br />From: Amit Choubey <kgp.amit@gmail.com><br />Subject: Re: [gmx-users] trjconv with multiple chains<br />To: Discussion list for GROMACS users <gmx-users@gromacs.org><br />Message-ID:<br /> <AANLkTi=2=NfWA_budToyKiXZT5rdXRGNk7RHzXvN7bc=@mail.gmail.com><br />Content-Type: text/plain; charset="iso-8859-1"<br /><br />Make your box bigger?<br /><br />2011/1/6 yuanyuan wang <yilin3201@126.com><br /><br />> dear all,<br />> I am doing a simulation that have many chains in a box , and I can<br />> find a center for them after serval tries.<br />> I use almost every option of trjconv,-pbc<br />> mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box,<br />> and -boxcenter, -fit ..<br />> still some chain cannot convert into box. them jump
from one box<br />> to another ,<br />> is there any ways that they not jump to another box?<br />> thanks a lot.<br />><br />><br />> yuanyuan<br />><br />><br />><br />> --<br />> gmx-users mailing list gmx-users@gromacs.org<br />> http://lists.gromacs.org/mailman/listinfo/gmx-users<br />> Please search the archive at<br />> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br />> Please don't post (un)subscribe requests to the list. Use the<br />> www interface or send it to gmx-users-request@gromacs.org.<br />> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br /></div><br /><br /><span title="neteasefooter"><span id="netease_mail_footer"></span></span></div></blockquote>