[gmx-users] genion question

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> 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!
> 

The total charge will undoubtedly fluctuate.  What's most important to look at 
is when you reach the end of a residue and you do not see an integer charge.

-Justin

> 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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> 
> 

-- 
========================================

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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