[gmx-users] genion question

[Paymon Pirzadeh]

Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure if I can attach the .top file to my e-mail for you to
check. This way I could learn where and how things go wrong!

Payman








On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Thanks for the tips!
> > But I still have problem with my added ion. Justin had told me that ion
> > names are force-field specific! Since I am using OPLSaa, I checked the
> > itp file for Na ion name, and it was Na+. I used this name with the
> 
> No, it's not.  It's NA+.  From ions.itp in the #ifdef _FF_OPLS section:
> 
> [ moleculetype ]
> ; molname       nrexcl
> NA+             1
> 
> [ atoms ]
> ; id    at type         res nr  residu name     at name  cg nr  charge   mass
> 1       opls_407        1       NA+             NA       1      1       22.98977
> 
> > -pname switch, but again during the grompp I ran into the following
> > error:
> > Warning: atom name 65870 in AFP_I.top and
> > AFP_I_solvated_54_62_102_null.gro does not match (NA - Na)
> > 
> > WARNING 1 [file AFP_I.top, line 4151]:
> >   1 non-matching atom name
> >   atom names from AFP_I.top will be used
> >   atom names from AFP_I_solvated_54_62_102_null.gro will be ignored
> > 
> > I really do not know what I am doing wrong here! Also regarding past
> > discussions, adding this single ion has lead into the following note:
> >  
> > NOTE 1 [file AFP_I.top, line 4151]:
> >   System has non-zero total charge: 1.000000e-02
> > 
> > I am not sure if that much charge will cause me troubles or not!
> > 
> 
> I am somewhat troubled by the magnitude of charge discrepancy.  Look in the .top 
> to see where things start going wrong (i.e., not an integer).  I would think 
> your system would have to be quite large to accumulate such a difference in charge.
> 
> -Justin
> 
> > Payman
> > 
> > 
> > 
> > 
> > 
> > On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote:
> >> Paymon Pirzadeh wrote:
> >>> Can I change the charge of Na ion added from +1 to +0.99 to cancel the
> >>> negative charge exactly? Does that hurt science or simulation?
> >> It's probably irrelevant. The representation of "decimal" numbers on 
> >> computers can be inexact, such that things like 0.02 added to itself 100 
> >> times does not pass a test for equality with 2. You may be observing 
> >> this kind of thing here. Your protein's [atoms] directive has a running 
> >> count of the total  charge on the molecule - go and read it and see that 
> >> each residue has an integral charge. Hopefully you can observe where the 
> >> rounding error might be occurring and you can make a judgement about 
> >> whether this might be true.
> >>
> >> Mark
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