[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 5 19:01:51 CET 2008
Chih-Ying Lin wrote:
> 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:
> 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!
> Thank you
> Chih-Ying Lin wrote:
>> 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.
>> Thank you
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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