Hi, I think there is no point in exactly copying the way a certain program treats things technically, except for checking force field implementation, but since that can be done without cut-off's there no real need. Charge groups are an ancient leftover from the old times when plain cut-off's were used. I don't actually know if Charmm uses charge groups with PME. But having no charge-groups at all leads to no artifacts, so that's the best solution anyhow.
I will try to completely get rid of charge groups in Gromacs in the next major release, so we get rid of these issues once and for all. Berk > Date: Fri, 17 Sep 2010 14:12:51 +0100 > From: t.pig...@soton.ac.uk > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1 > > Hi Berk and others, > > I have been wondering if there was another way to treat the large charge > groups for the CHARMM forcefield(s) in GROMACS, rather than using the > -nochargegrp option. > > The reason I ask is because changing every atom to be in individual > charge groups changes the forcefield (albeit slightly) from its original > implementation and it would be good to be able to use the forcefields in > as close a way as possible as to how they were originally used in CHARMM. > > I suppose another way to do it is to increase the cutoff's, however > changing the cutoff's from their original intended values is also > undesirable and this can also significantly impact on performance. > Whether this is better or worse (in the sense of the difference to how > the forcefields were originally used in CHARMM) than using -nochargegrp > I am not sure. I also noticed that in version 4.5 there is a rlistlong > parameter, could this be used to account for the large charge groups > rather than increasing other cutoff's? > > Can anyone think of any other ways to do this? I have no idea if it be > easy/possible to implement an option to use the CHARMM approach for > treating charge groups (as I understand it when any atom is within the > cutoff then the whole charge group is included). > > Sorry for the fairly long message and thanks for any insights you can give. > > Tom > > Berk Hess wrote: > > Hi, > > > > No, you should never change the charges in a force field! > > > > Run pdb2gmx again with the -nochargegrp option. > > That will make the size of all charge groups a single atom. > > This will be done automatically in the 4.5.2 release which will be out soon. > > > > Berk > > > > ------------------------------------------------------------------------ > > Date: Fri, 17 Sep 2010 02:32:31 -0700 > > From: meetnah...@yahoo.com > > To: gmx-users@gromacs.org > > Subject: [gmx-users] ARG Charmm gmx 4.5.1 > > > > Dear Gromacs Users, > > > > I am using plain cutoff for my 12-mer protein. > > The grompp reports ARG to have a big charge group. this was also > > highlighted in the following mail > > http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html > > > > I was just think if changing the charges on these atoms would help, > > from > > 13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2 > > 14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29 > > 15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38 > > 16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68 > > 17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12 > > 18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76 > > 19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96 > > 20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42 > > 21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88 > > 22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08 > > 23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54 > > 24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2 > > > > > > to > > > > CD 0.18 > > HD1 0.06 > > HD2 0.06 > > NE -0.7 > > HE 0.4 > > CZ 0.6 > > NH1 -0.8 > > HH11 0.5 > > HH12 0.5 > > NH2 -0.8 > > HH21 0.5 > > HH22 0.5 > > > > The above transformation of charges seems reasonable. > > > > Would like to know if this is okay... > > > > > > Best, > > nahren > > > > > > > > > > -- gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the > > archive at http://www.gromacs.org/Support/Mailing_Lists/Search before > > posting! Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. Can't post? > > Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Dr Thomas Piggot > University of Southampton, UK. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists