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<body class='hmmessage'><br><br><br><br><hr id="stopSpelling">> Date: Thu, 9 Oct 2008 08:44:15 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] steady<br>> <br>> <br>> <br>> shahrbanoo karbalaee wrote:<br>> > Dear justin<br>> > <br>> > a) if I want to have the steady and hemogen for mix solvent , do I<br>> > have to use this command (when I made genbox box 16.16.24 before<br>> > that)?<br>> > :editconf -f conf.gro -bt dodecahedron -d 0.5 -o box.gro<br>> <br>> This will not homogenize anything; it only sets up the initial system. To get a <br>> homogeneous box you have to equilibrate (sometimes for a very long time).<br>> <br>> > b) I use trjconv -pbc mol -ur compact and then minimize .when I see<br>> > the output this part in vmd or ngmx and around X-rotate.I will see<br>> > water in top and tfe in down box and another roatation the box is<br>> > seemed hemogen ous .is it correct?<br>> <br>> No. Using -pbc mol -ur compact is a post-processing trick to visualize. If you <br>> use the trjconv output in a simulation, it's likely to go screwy, since Gromacs <br>> determines periodicity from a triclinic unit cell.<br>> <br>> Create your system (using -bt dodecahedron is fine, but will likely look like a <br>> rectangle in VMD or ngmx), and minimize. Use the output of the minimization for <br>> your equilibration simulations. If you want to visualize a dodecahedral box, <br>> then use trjconv, but do not use this altered file for simulations.<br>> <br>> -Justin<br>> <br><br>This post processing by trjconv with -pbc and -ur only changes which periodic<br>copy of a molecule or group is used.<br>Such configurations can be used for simulations without problems,<br>since the actual structure did not change.<br>mdrun will put things back in the periodic cell it wants at startup<br>(unless the continuation is turned on in Gromacs 4).<br><br>Berk<br><br>> > about distortion ,my mean is"donot have periodicity and hemogenity"<br>> > <br>> > thanks and appreiciate u<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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