[gmx-users] genion question
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 26 00:15:13 CEST 2009
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
[ 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
> 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.
> 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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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