<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>You can not do much.<br>The reason for this error message is also valid for older versions.<br>It can not be guaranteed that the virtual sites in one charge group will<br>have the same periodic shift. But before 4.0 there was no check for this.<br><br>I would simply not use vsite aromatics. I am in favor of completely<br>removing this option from pdb2gmx, since you do not gain so much<br>compared with dt=4 or 5 fs with -vsite h (and optionally heavy hydrogens).<br><br>If you really want to use the vsite aromatics, you can put all atoms<br>in the aromatic groups in separate charge groups, but that will make<br>the simulation slightly slower.<br><br>Berk<br></div><br><br><hr id="stopSpelling">> Date: Tue, 4 Nov 2008 02:45:13 -0800<br>> From: zazeri@yahoo.com.br<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] vsite problem in gromacs 4.0<br>> <br>> Hi gmx-users!<br>> <br>> I've created the topology of a peptide using pdb2gmx(4.0-rc4) converting aromatic rings into virtual sites. I've used the grompp(4.0_rc4) to compile the input for the mdrun and it was ok, no error message, but<br>> when running mdrun(4.0-rc4):<br>> <br>> Program mdrun4, VERSION 4.0_rc4<br>> Source code file: vsite.c, line: 1504<br>> <br>> Fatal error:<br>> Virtual site atom 29 is part of a charge group of only virtual sites, but its first constructing atom (26) is part of a different charge group, this combination is not allowed.<br>> <br>> I've repeated the process using grompp(3.3.1), mdrun(3.3.1) and the same topology (it was created by pdb2gmx(4.0-rc4)) and the simulation run well.<br>> <br>> What could I do? I'd like enjoy the new implementations in PME from gromacs 4.0! Any suggestion would be appreciated, thanks. Fernando "Zazeri" Lopes.<br>> <br>> <br>> A little part from my topology (as GROMOS87):<br>> 23 N 3 TRP N 12 -0.28 15.0147<br>> 24 H 3 TRP H 12 0.28 0<br>> 25 CH1 3 TRP CA 13 0 13.019<br>> 26 MW 3 TRP MW1 14 0 52.0557<br>> 27 MW 3 TRP MW2 14 0 64.087<br>> 28 CH2 3 TRP CB 15 0 14.027<br>> 29 CB 3 TRP CG 16 -0.14 0<br>> 30 CR5 3 TRP CD1 16 -0.14 0<br>> 31 HCR 3 TRP HD1 16 0.14 0<br>> 32 CB 3 TRP CD2 16 0 0<br>> 33 NR5* 3 TRP NE1 16 -0.05 0<br>> 34 H 3 TRP HE1 16 0.19 0<br>> 35 CB 3 TRP CE2 17 0 0<br>> 36 CR6 3 TRP CE3 18 -0.14 0<br>> 37 HCR 3 TRP HE3 18 0.14 0<br>> 38 CR6 3 TRP CZ2 19 -0.14 0<br>> 39 HCR 3 TRP HZ2 19 0.14 0<br>> 40 CR6 3 TRP CZ3 20 -0.14 0<br>> 41 HCR 3 TRP HZ3 20 0.14 0<br>> 42 CR6 3 TRP CH2 21 -0.14 0<br>> 43 HCR 3 TRP HH2 21 0.14 0<br>> 44 C 3 TRP C 22 0.38 12.011<br>> 45 O 3 TRP O 22 -0.38 15.9994<br>> <br>> <br>> <br>> Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com.<br>> http://br.new.mail.yahoo.com/addresses<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>
</html>