[gmx-users] ARG Charmm gmx 4.5.1

[Berk Hess]

Hi,

The choice of charge is significant even with PME, because of the way
Gromacs makes the neighborlists.

As I mailed before, use the -nochargegrp option of pdb2gmx with the Charmm27 ff.

Berk

> Date: Fri, 17 Sep 2010 11:46:36 +0200
> From: qiaobf at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1
> 
> 
> You  should change the charge group number. Every charge group include
> several, like 3-4, atoms. Actually, the definition of charge group is
> not significant if you use PME for the coulomb interaction.
> 
> 
> nahren manuel wrote:
> > 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 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100917/0420ebd3/attachment.html>