[gmx-users] ARG Charmm gmx 4.5.1
gmx3 at hotmail.com
Fri Sep 17 15:46:56 CEST 2010
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.
> 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.
> 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://email@example.com/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
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> Dr Thomas Piggot
> University of Southampton, UK.
> gmx-users mailing list gmx-users at gromacs.org
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