[gmx-users] VDW radii of Br and K+

[nishap.patel at utoronto.ca]

Thanks! I did overlook that.


Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On 2010-08-24 22.53, nishap.patel at utoronto.ca wrote:
>> Hello,
>>
>> I converted a .tpr file for Bromine ion and Potassium ion using -mead
>> option and editconf. It gives out the Van der Waals radius of the atom,
>> but I don't understand why i got ~2.46A for Potassium and ~2.31A for
>> Bromide. Isn't the bromide ion bigger than Potassium? And I used genion
>> to add both the atoms.
> This is a force field quirk. From the oplsaa.ff/ffnonbonded.itp
>
> [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ; name  bond_type    mass    charge   ptype          sigma      epsilon
> opls_402  Br- 35 79.90400    -1.000       A    4.62376e-01  3.76560e-01
> opls_408  K+  19 39.09830     1.000       A    4.93463e-01  1.37235e-03
>
> You see that K+ has larger sigma than Br-.
>
>
>>
>> Thanks.
>>
>> -Nisha P
>>
>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
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