[gmx-users] ARG Charmm gmx 4.5.1

[Berk Hess]

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.piggot at soton.ac.uk
> To: gmx-users at 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: meetnahren at yahoo.com
> > To: gmx-users at 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 at gromacs.org 
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> > 
> 
> -- 
> Dr Thomas Piggot
> University of Southampton, UK.
> -- 
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