[gmx-users] ARG Charmm gmx 4.5.1
Berk Hess
gmx3 at hotmail.com
Fri Sep 17 16:10:44 CEST 2010
Hi,
I just got a mail from a CHARMM developer saying that charge groups in CHARMM
have no influence on the way forces are calculated.
The details of the use of charge groups in CHARMM are not how I guessed they were,
but the conclusion is that one should use no charge groups (or single atom charge groups
to be more precise) for the CHARMM force field in Gromacs.
Berk
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] ARG Charmm gmx 4.5.1
Date: Fri, 17 Sep 2010 15:46:56 +0200
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
> > http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
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> >
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
> --
> gmx-users mailing list gmx-users at gromacs.org
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