<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Ah, sorry, the email I replied to does not contain the whole history.<br><br>There are only issues with vsite aromatics in Gromacs 4.0<br>(and they will cause a fatal error or segv, no incorrect results).<br>All other applications of virtual sites are unaffected.<br><br>Berk<br><br><hr id="stopSpelling">From: larsson@xray.bmc.uu.se<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] RE: vsite problem in gromacs 4.0<br>Date: Thu, 6 Nov 2008 17:45:47 +0100<br><br><br><div><div>On Nov 6, 2008, at 14:48 , Berk Hess wrote:</div><br class="EC_Apple-interchange-newline"><blockquote><span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div class="EC_hmmessage" style="font-size: 10pt; font-family: Verdana;">Hi,<br><br>I fixed the virtual site charge group issue in mdrun for 4.0.1.<br>Now vsite aromatics will run fine.<br><br>But there is still an issue in pdb2gmx for some proteins<br>when selecting the OPLS force field.<br>I hope we can fix this for 4.0.1.</div></span></blockquote><div><br></div><div>Is it something serious? When does it occur?</div><br><blockquote><span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div class="EC_hmmessage" style="font-size: 10pt; font-family: Verdana;">Berk<br><br>> Date: Tue, 4 Nov 2008 11:32:46 -0500<br>> From:<span class="EC_Apple-converted-space"> </span><a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a><br>> To:<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Subject: [gmx-users] RE: vsite problem in gromacs 4.0<br>><span class="EC_Apple-converted-space"> </span><br>> Hi Berk,<br>><span class="EC_Apple-converted-space"> </span><br>> I have taken the information from these posts and created a wiki page<span class="EC_Apple-converted-space"> </span><br>> on the topic:<span class="EC_Apple-converted-space"> </span><br>><span class="EC_Apple-converted-space"> </span><a href="http://wiki.gromacs.org/index.php/Removing_fastest_degrees_of_freedom">http://wiki.gromacs.org/index.php/Removing_fastest_degrees_of_freedom</a><br>><span class="EC_Apple-converted-space"> </span><br>> However, I was unable to add a link to<span class="EC_Apple-converted-space"> </span><br>><span class="EC_Apple-converted-space"> </span><a href="http://wiki.gromacs.org/index.php/Category:Beginners">http://wiki.gromacs.org/index.php/Category:Beginners</a><span class="EC_Apple-converted-space"> </span>as the edit tab<span class="EC_Apple-converted-space"> </span><br>> only allowed me to edit the top content of that page, and not the<span class="EC_Apple-converted-space"> </span><br>> subcategories.<br>><span class="EC_Apple-converted-space"> </span><br>> If you have time to edit this new page then that would be great. Also,<span class="EC_Apple-converted-space"> </span><br>> if anybody knows how to link it then that would also be great.<br>><span class="EC_Apple-converted-space"> </span><br>> Thanks,<br>> Chris.<br>><span class="EC_Apple-converted-space"> </span><br>><span class="EC_Apple-converted-space"> </span><br>> _______________________________________________<br>> gmx-users mailing list<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>><span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="EC_Apple-converted-space"> </span>before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<span class="EC_Apple-converted-space"> </span><br>> www interface or send it to<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><hr>Express yourself instantly with MSN Messenger!<span class="EC_Apple-converted-space"> </span><a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a><span class="EC_Apple-converted-space"> </span>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="EC_Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="EC_Apple-converted-space"> </span><br>www interface or send it to<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><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>
</html>