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Hi,<br><br>The choice of charge is significant even with PME, because of the way<br>Gromacs makes the neighborlists.<br><br>As I mailed before, use the -nochargegrp option of pdb2gmx with the Charmm27 ff.<br><br>Berk<br><br>> Date: Fri, 17 Sep 2010 11:46:36 +0200<br>> From: qiaobf@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1<br>> <br>> <br>> You should change the charge group number. Every charge group include<br>> several, like 3-4, atoms. Actually, the definition of charge group is<br>> not significant if you use PME for the coulomb interaction.<br>> <br>> <br>> nahren manuel wrote:<br>> > Dear Gromacs Users,<br>> ><br>> > I am using plain cutoff for my 12-mer protein.<br>> > The grompp reports ARG to have a big charge group. this was also highlighted in the following mail<br>> > http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html<br>> ><br>> > I was just think if changing the charges on these atoms would help,<br>> > from<br>> > 13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2<br>> > 14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29<br>> > 15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38<br>> > 16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68<br>> > 17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12<br>> > 18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76<br>> > 19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96<br>> > 20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42<br>> > 21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88<br>> > 22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08<br>> > 23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54<br>> > 24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2<br>> ><br>> ><br>> ><br>> > to<br>> ><br>> ><br>> ><br>> ><br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > CD 0.18<br>> > HD1 0.06<br>> > HD2 0.06<br>> > NE -0.7<br>> > HE 0.4<br>> > CZ 0.6<br>> > NH1 -0.8<br>> > HH11 0.5<br>> > HH12 0.5<br>> > NH2 -0.8<br>> > HH21 0.5<br>> > HH22 0.5<br>> ><br>> > The above transformation of charges seems reasonable.<br>> ><br>> > Would like to know if this is okay...<br>> ><br>> ><br>> > Best,<br>> > nahren<br>> ><br>> ><br>> ><br>> ><br>> ><br>> > <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/Support/Mailing_Lists/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/Support/Mailing_Lists<br> </body>
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