<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> 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>