<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
Thank you very much.<br>One question, how should I use it? Should I compile Gromacs again?<br>Cheers,<br>Rebeca.<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: jalemkul@vt.edu; gmx-users@gromacs.org<br>Subject: RE: [gmx-users] problem in g_rdf using only x and y<br>Date: Wed, 24 Feb 2010 15:29:49 +0100<br>CC: <br><br>
<style>
.ExternalClass .ecxhmmessage P
{padding:0px;}
.ExternalClass body.ecxhmmessage
{font-size:10pt;font-family:Verdana;}
</style>
Hi,<br><br>I realize now that I committed a fix for this bug 3 days after the release<br>of 4.0.7 (and not 3 days before the release as I initially thought).<br><br>If you need it right now, I put the fixed source at:<br>http://hess.cbr.su.se/~hess/gmx_rdf.c<br><br>Berk<br><br>> Date: Wed, 24 Feb 2010 06:52:57 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] problem in g_rdf using only x and y<br>> <br>> <br>> <br>> Berk Hess wrote:<br>> > Well, I fixed a bug with g_rdf -xy before the 4.0.7 release.<br>> > But apparently this fix does not work under all conditions.<br>> > Could one of you file a bugzilla and attach a tpr file and a trajectory,<br>> > preferably with only one or very few frames and write the exact command <br>> > line?<br>> <br>> Filed as bugzilla #399. I uploaded a .tpr and .gro that reproduce the error; if <br>> you want an actual (small) trajectory, I can provide that as well.<br>> <br>> -Justin<br>> <br>> > <br>> > Thanks,<br>> > <br>> > Berk<br>> > <br>> > > Date: Tue, 23 Feb 2010 13:51:39 -0500<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] problem in g_rdf using only x and y<br>> > ><br>> > ><br>> > ><br>> > > Rebeca García Fandiño wrote:<br>> > > > Hi,<br>> > > > thank you very much for your answer. However, I have tried with the<br>> > > > 4.0.7 version, and the problem continues, and it is just the same. I<br>> > > > have the trajectory and tpr file obtained with the 4.0.4 version. <br>> > Do you<br>> > > > think it cares, or maybe is it another problem?<br>> > ><br>> > > I think there is a problem in g_rdf, not a 4.0.4 vs 4.0.7 issue. I <br>> > was actually<br>> > > about to report this problem, myself. I have simulations that I did with<br>> > > version 4.0.7, and the RDF analysis hung the exact same way as you <br>> > reported.<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Cheers,<br>> > > > Rebeca.<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > From: gmx3@hotmail.com<br>> > > > To: gmx-users@gromacs.org<br>> > > > Subject: RE: [gmx-users] problem in g_rdf using only x and y<br>> > > > Date: Tue, 23 Feb 2010 16:47:43 +0100<br>> > > ><br>> > > > Hi,<br>> > > ><br>> > > > I fixed this bug in 4.0.7.<br>> > > ><br>> > > > Berk<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > From: regafan@hotmail.com<br>> > > > To: gmx-users@gromacs.org<br>> > > > Date: Tue, 23 Feb 2010 15:40:07 +0000<br>> > > > Subject: [gmx-users] problem in g_rdf using only x and y<br>> > > ><br>> > > > Hi,<br>> > > > I am trying to calculate g_rdf using only the x and y components of <br>> > the<br>> > > > distance (gromacs 4.0.4):<br>> > > ><br>> > > > g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o <br>> > rdf_Na_xy.xvg<br>> > > > -com -norm -pbc -xy and the calculations stays at the window:<br>> > > ><br>> > > > Select a group: 1<br>> > > > Selected 1: 'UNK'<br>> > > > Select a group: 4<br>> > > > Selected 4: 'Na'<br>> > > > Reading frame 0 time 0.000<br>> > > ><br>> > > > for days...(I had to kill it after 4 days).<br>> > > ><br>> > > > Using the same order without -xy takes only 10 minutes.<br>> > > ><br>> > > > Is there anything wrong with the commands I am using? Or maybe is <br>> > there<br>> > > > a bug in the -xy option?<br>> > > ><br>> > > > Thank you very much for your help, in advance.<br>> > > ><br>> > > > Best wishes,<br>> > > ><br>> > > > Rebeca Garcia.<br>> > > > <http://serviciosmoviles.es.msn.com/hotmail/movistar.aspx><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > ¿Quieres tener a tus amigos de Facebook en Messenger? ¡Clic AQUÍ!<br>> > > > <http://vivelive.com/feedfacebook/><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > New Windows 7: Find the right PC for you. Learn more.<br>> > > > <http://windows.microsoft.com/shop><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > Navega con el navegador más seguro de todos. ¡Descárgatelo ya!<br>> > > > <http://www.vivelive.com/internetexplorer8><br>> > > ><br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Ph.D. Candidate<br>> > > ICTAS Doctoral Scholar<br>> > > MILES-IGERT Trainee<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://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > 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>> > New Windows 7: Find the right PC for you. Learn more. <br>> > <http://windows.microsoft.com/shop><br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<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://lists.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>New Windows 7: Find the right PC for you. <a href="http://windows.microsoft.com/shop">Learn more.</a>                                            <br /><hr />Disfruta de un resumen diario de tu Hotmail en tu móvil Movistar. <a href='http://serviciosmoviles.es.msn.com/hotmail/movistar.aspx' target='_new'>¡Accede ya!</a></body>
</html>