[gmx-users] re K+ ion

[taveechai taveecharoenkool]

Dear Yang,
 Thanks again.
i got this line
atom[ 52281]={type= 25, typeB= 25, ptype=    Atom, m=
3.90983e+01, q= 1.00000e+00, mB= 3.90983e+01, qB=
1.00000e+00, resnr=13633} grpnrs=[ 3 3 0 0 0 0 0 0 0
]}
which should mean my K+ has +1 charge. and there is no
NB interaction from
excl[52281][211661..211661]={52281}. Now , i just
wonder when i use g_saltbr it doesn't say interaction
of K+ and CL- ions. My system contains 488 K+ and 488
CL-.

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

> taveechai taveecharoenkool wrote:
> > 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,
> >   
> excl[0][0...5] means for atom #0 (find this in your
> gro file) has 6 
> exclusion respectively to atom #0, #1, #2,...,#5.
> In your problem, you may locate the atom # for K and
> find its' exclusion 
> list. Exclusion means there is no NB interaction
> between the pair.
> You can also check the charge for K in the dump
> file.
> > --- 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
> >> /
> >>
> >>     
> >
> >
> > __________________________________________________
> 
=== message truncated ===


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