[gmx-users] ARG Charmm gmx 4.5.1

[Thomas Piggot]

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
> 
> 
> 
> 
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-- 
Dr Thomas Piggot
University of Southampton, UK.