<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
Hi,<br><br>Are you 100% sure you have no other charge groups in your system<br>that consist of only virtual sites, but at least with 2 virtual sites?<br><br>I just fixed a bug with this situation for 4.0.6 and 4.1.<br>You can try the git master or 4.0 release branch.<br><br>I don't understand why only your terminal NH3 becomes a single charge group,<br>unless the hydrogens were generated with the .hdb file,<br>while they were present for all other NH3 groups.<br><br>Berk<br><br>> Date: Wed, 30 Sep 2009 16:45:39 +0200<br>> From: jochen@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes<br>> <br>> Hey Berk,<br>> <br>> I just found that the simulation with a separate CG on each atom also <br>> crashed, but much later (after 11ns), that why I just noticed that. I <br>> have repeated the simulations now to make really sure that the crashes <br>> are reproducible.<br>> <br>> Jochen<br>> <br>> <br>> Jochen Hub wrote:<br>> ><br>> > I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting <br>> > else?<br>> ><br>> > Jochen<br>> ><br>> ><br>> > Berk Hess wrote:<br>> >> Hi,<br>> >><br>> >> One question:<br>> >> Are these crashes single processor, with domain decomposition, or both?<br>> >><br>> >> Berk<br>> >><br>> >> > Date: Wed, 30 Sep 2009 15:35:42 +0200<br>> >> > From: jochen@xray.bmc.uu.se<br>> >> > To: gmx-users@gromacs.org<br>> >> > Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, <br>> >> and crashes<br>> >> ><br>> >> > Hi,<br>> >> ><br>> >> > I have been trying to use vsites with AMBER99SB, but the simulation<br>> >> > frequently cashes after a few hundred ps with the suspects (lincs<br>> >> > warnings, 1-4 distance error). I could pinpoint the problem to <br>> >> erroneous<br>> >> > charge group assignments generated by pdb2gmx at the NH3 group at the<br>> >> > N-terminus. The following charge group assignments caused the error:<br>> >> ><br>> >> > ; nr type resnr residue atom cgnr charge mass<br>> >> > 1 MNH3 1 NASN MN1 1 0 8.517 ;<br>> >> > qtot 0<br>> >> > 2 MNH3 1 NASN MN2 1 0 8.517 ;<br>> >> > qtot 0<br>> >> > 3 amber99_39 1 NASN N 1 0.1801 0 ;<br>> >> > qtot 0.1801<br>> >> > 4 amber99_17 1 NASN H1 2 0.1921 0 ;<br>> >> > qtot 0.3722<br>> >> > 5 amber99_17 1 NASN H2 2 0.1921 0 ;<br>> >> > qtot 0.5643<br>> >> > 6 amber99_17 1 NASN H3 2 0.1921 0 ;<br>> >> > qtot 0.7564<br>> >> > 7 amber99_11 1 NASN CA 3 0.0368 13.018 ;<br>> >> > qtot 0.7932<br>> >> > ...<br>> >> ><br>> >> > The NH3 groups in the lysines were fine and did not cause any <br>> >> error. The<br>> >> > only difference compared to the N-terminus is that each of the three H<br>> >> > in the NH3 has its own charge group, but the vsites and the N are <br>> >> still<br>> >> > in the same CG:<br>> >> ><br>> >> > 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ;<br>> >> > qtot 0.9937<br>> >> > 31 amber99_28 2 LYP HE1 30 0.1135 0 ;<br>> >> > qtot 1.107<br>> >> > 32 amber99_28 2 LYP HE2 31 0.1135 0 ;<br>> >> > qtot 1.221<br>> >> > 33 MNH3 2 LYP MNZ1 32 0 8.517 ;<br>> >> > qtot 1.221<br>> >> > 34 MNH3 2 LYP MNZ2 32 0 8.517 ;<br>> >> > qtot 1.221<br>> >> > 35 amber99_39 2 LYP NZ 32 -0.3854 0 ;<br>> >> > qtot 0.8353<br>> >> > 36 amber99_17 2 LYP HZ1 33 0.34 0 ;<br>> >> > qtot 1.175<br>> >> > 37 amber99_17 2 LYP HZ2 34 0.34 0 ;<br>> >> > qtot 1.515<br>> >> > 38 amber99_17 2 LYP HZ3 35 0.34 0 ;<br>> >> > qtot 1.855<br>> >> ><br>> >> > Alternatively, I have also tried to give every single atom (including<br>> >> > the vsites MN??) a separate charge group, which also worked fine.<br>> >> ><br>> >> > 1)<br>> >> > So, is there any reason why the dummies should be in the same CG as <br>> >> the<br>> >> > nitrogen? Or should it be fine just to assign a separate CG to <br>> >> every atom?<br>> >> ><br>> >> > 2)<br>> >> > Is a bug report appreciated on that issue?<br>> >> ><br>> >> > Best,<br>> >> ><br>> >> > Jochen<br>> >> ><br>> >> ><br>> >> > --<br>> >> > ---------------------------------------------------<br>> >> > Dr. Jochen Hub<br>> >> > Molecular Biophysics group<br>> >> > Dept. of Cell & Molecular Biology<br>> >> > Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> >> > Phone: +46-18-4714451 Fax: +46-18-511755<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>> >> See all the ways you can stay connected to friends and family <br>> >> <http://www.microsoft.com/windows/windowslive/default.aspx><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 www <br>> >> 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>> ---------------------------------------------------<br>> Dr. Jochen Hub<br>> Molecular Biophysics group<br>> Dept. of Cell & Molecular Biology<br>> Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> Phone: +46-18-4714451 Fax: +46-18-511755<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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>