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Hi,<br><br>I think there is no point in exactly copying the way a certain program treats things technically,<br>except for checking force field implementation, but since that can be done without cut-off's<br>there no real need.<br>Charge groups are an ancient leftover from the old times when plain cut-off's were used.<br>I don't actually know if Charmm uses charge groups with PME.<br>But having no charge-groups at all leads to no artifacts, so that's the best solution anyhow.<br><br>I will try to completely get rid of charge groups in Gromacs in the next major release,<br>so we get rid of these issues once and for all.<br><br>Berk<br><br>> Date: Fri, 17 Sep 2010 14:12:51 +0100<br>> From: t.piggot@soton.ac.uk<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1<br>> <br>> Hi Berk and others,<br>> <br>> I have been wondering if there was another way to treat the large charge <br>> groups for the CHARMM forcefield(s) in GROMACS, rather than using the <br>> -nochargegrp option.<br>> <br>> The reason I ask is because changing every atom to be in individual <br>> charge groups changes the forcefield (albeit slightly) from its original <br>> implementation and it would be good to be able to use the forcefields in <br>> as close a way as possible as to how they were originally used in CHARMM.<br>> <br>> I suppose another way to do it is to increase the cutoff's, however <br>> changing the cutoff's from their original intended values is also <br>> undesirable and this can also significantly impact on performance. <br>> Whether this is better or worse (in the sense of the difference to how <br>> the forcefields were originally used in CHARMM) than using -nochargegrp <br>> I am not sure. I also noticed that in version 4.5 there is a rlistlong <br>> parameter, could this be used to account for the large charge groups <br>> rather than increasing other cutoff's?<br>> <br>> Can anyone think of any other ways to do this? I have no idea if it be <br>> easy/possible to implement an option to use the CHARMM approach for <br>> treating charge groups (as I understand it when any atom is within the <br>> cutoff then the whole charge group is included).<br>> <br>> Sorry for the fairly long message and thanks for any insights you can give.<br>> <br>> Tom<br>> <br>> Berk Hess wrote:<br>> > Hi,<br>> > <br>> > No, you should never change the charges in a force field!<br>> > <br>> > Run pdb2gmx again with the -nochargegrp option.<br>> > That will make the size of all charge groups a single atom.<br>> > This will be done automatically in the 4.5.2 release which will be out soon.<br>> > <br>> > Berk<br>> > <br>> > ------------------------------------------------------------------------<br>> > Date: Fri, 17 Sep 2010 02:32:31 -0700<br>> > From: meetnahren@yahoo.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: [gmx-users] ARG Charmm gmx 4.5.1<br>> > <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 <br>> > 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>> > to<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>> > -- gmx-users mailing list gmx-users@gromacs.org <br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the <br>> > archive at http://www.gromacs.org/Support/Mailing_Lists/Search before <br>> > posting! Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org. Can't post? <br>> > Read http://www.gromacs.org/Support/Mailing_Lists<br>> > <br>> <br>> -- <br>> Dr Thomas Piggot<br>> University of Southampton, UK.<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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