<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 9pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'>
Thanks for your reply. I just checked the online manual for .mdp. But I didn't find<br>an option to change output pbc types. If I need the output trr file to be "whole" as<br>that from an older version, can I set it up anywhere?<br>I understand I can use trjconv to convert trr files. But usually trr files are huge and<br>the convertion takes time.<br>Thanks,<br>Lanyuan Lu<br><br>> Date: Mon, 28 Jul 2008 17:07:30 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories?<br>> <br>> <br>> <br>> LuLanyuan wrote:<br>> > Hello,<br>> > I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x.<br>> > The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc.<br>> > As I remember for early versions of Gromacs the default pbc of output trajectories was "whole",<br>> > which means no broken molecules. But I just found it's not the case for the latest version, since<br>> > I can see broken lipids for my membrane system using "ngmx". I'm just wondering what's the<br>> > default pbc for the latest Gromacs version and whether there is a way to change it before MD<br>> > simulations.<br>> <br>> I think you are asking two separate questions.<br>> <br>> From trjconv -h you can find the default behavior for PBC treatment, which is <br>> "none," as in, leave the coordinates alone.<br>> <br>> The PBC behavior of an MD simulation is specified in the .mdp file. Removal of <br>> PBC from "broken" starting structures should be the first step in the simulation.<br>> <br>> -Justin<br>> <br>> > Thanks for your help.<br>> > Lanyuan Lu<br>> > _________________________________________________________________<br>> > MSN 中文网，最新时尚生活资讯，白领聚集门户。<br>> > http://cn.msn.com<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>> <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 />使用新一代 Windows Live Messenger 轻松交流和共享！ <a href='http://messenger.live.cn/' target='_new'>立即体验！</a></body>
</html>