[gmx-users] re K+ ion

[taveechai taveecharoenkool]

Hi Yang,
 I don't understand what you mean, please give me an
example.
i see 
 excl:
            multinr[division over processors]: 52414 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0
            nr=52414
            nra=211794
            excl[0][0..5]={0, 1, 2, 3, 4, 5}
            excl[1][6..13]={0, 1, 2, 3, 4, 5, 6, 18}
            excl[2][14..19]={0, 1, 2, 3, 4, 5}
            excl[3][20..30]={0, 1, 2, 3, 4, 5, 6, 7,
18, 19, 20}
            excl[4][31..38]={0, 1, 2, 3, 4, 5, 6, 18}
what does this mean?
Please help,

--- Yang Ye <leafyoung81-group at yahoo.com> wrote:

> use gmxdump -s to check whether there is exclusion
> between them (look 
> for "excl")
> 
> taveechai taveecharoenkool wrote:
> > Dear Jochen,
> > thanks very much for your reply. Anyway, i already
> did
> > what you suggest. I can run without the problem. I
> > want to analyze the system after 1ns or 2ns, when
> i
> > use g_saltbr which tell the oppositely two-charged
> > groups. it doesn't have interaction of K+ and
> negative
> > charge. I quite don't understand.. where my K+
> charge.
> >
> >
> > --- Jochen Hub <jhub at gwdg.de> wrote:
> >
> >   
> >> taveechai taveecharoenkool wrote:
> >>
> >>     
> >>> Dear all,
> >>> I want to study the effect of K ion on a
> protein.
> >>>       
> >> I
> >>     
> >>> add this line in ions.itp 
> >>> [ moleculetype ]
> >>> ; molname	nrexcl
> >>> K+		1
> >>> [ atoms ]
> >>> ; id	at type res nr	residu name	at name  cg nr 
> >>>       
> >> charge
> >>     
> >>>  mass
> >>> 1	K+	1	K+		K	1	1	 39.0983  
> >>> it seems ok, i can run (mdrun) without error.
> The
> >>> thing in my mind is that is it enough (to edit
> only
> >>> one file) cos it seems like K+ doesn't contain
> >>> positive charge when i used g_saltbr? i use
> >>>       
> >> Gromos96
> >>     
> >>> forcefield.
> >>> Thanks in advance
> >>>
> >>>       
> >> You should add a
> >> K+      1
> >>
> >> into the [ molecules ] section of your topol.top.
> >>
> >> And , of course, you need to place it into your
> >> starting structure (pdb 
> >> or gro).
> >>
> >> Jochen
> >>
> >> -- 
> >> ************************************************
> >> Jochen Hub
> >> Max Planck Institute for Biophysical Chemistry
> >> Computational biomolecular dynamics group
> >> Am Fassberg 11
> >> D-37077 Goettingen, Germany
> >> Email: jhub[at]gwdg.de
> >> ************************************************
> >>
> >>
> >>
> >>     
> >
> >
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> 
> -- 
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> /
> 


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