[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> There is no BR- ion defined in ions.itp.
> Justin suggested "Proper parameterization is an extensive procedure".
> 
> As I checked the FFG53a6nb.itp, there are many sets of parameters
> between atoms. I might get the sets of force field parameters for Br-
> , something as described by FFG53a6nb.itp.
>

Within Gromos96 53a6, only the non-ionic bromine has been parameterized, as 
indicated in the .atp file, atom type BR (non-ionic).


> How to do "Proper parameterization" with a more understandable method?
> 

A literature search for the Gromos96 force fields will provide you with many 
references on the required simulations.

As a general bit of information to get you started:

http://wiki.gromacs.org/index.php/Parameterization

> 
> If the solution is very dilute, Br - ions will have very limited power
> affecting the whole system, I suppose. Are there any alternative ways
> to solve the problem ?
> 

Are you sure?  If Br- is unlikely to have much of an effect on the dynamics, 
then why not use Cl-, which is parameterized?  Be careful of deciding what's 
going to happen within your system before you actually simulate it; life has a 
funny way of proving us wrong!

-Justin

> Thank you
> Lin
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Chih-Ying Lin wrote:
>> Hi
>> In the ions.itp, there is no BR- ion defined  (FF_Gromos 96).
>>
>> But, it was defined in FF_OPLS.
>>
>> How did people solve the problem?
>> Could I simply use all of  BR-atom (assign it a -1 charge) non-bonded
>> parameters in FF_Gromos96 instead?
>>
> 
> No.  Assigning parameters is far more complicated that picking and choosing and
> putting them in whatever force field you wish you use.  Proper parameterization
> is an extensive procedure.
> 
> -Justin
> 
>> Thank you
>> Lin
>> _________________
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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