[gmx-users] genion question

Paymon Pirzadeh ppirzade at ucalgary.ca
Wed Aug 26 00:02:40 CEST 2009

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
-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!


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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