[gmx-users] genion question

[Justin A. Lemkul]

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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> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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