[gmx-users] Re: gromacs

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the message to the list; please continue any 
future discussion there.

See comments below.

Miroslawa aleksandrowa wrote:
> Dear Justin, My name is Miroslava Nedyalkova from Sofia University, Bulgaria.
> I am usuing GROMACS since 6 months. I think that is really great program ,but
> I have some problems :( I want to ask you for help, my problems are force
> field. Till now I was make calculations with methane sphere with Na and Ca2+
> ions with different concentrations of ions, I do this investigation with goal
> to study overcharging procession on the methane sphere surface . But now the
> problem :) I want to study process with overcharging with 3+ ions, like Fe.
> To this moment with Na and Ca 2+ ions I used G4a13 ans SPC model for water.
> My question is what do you thing for  using OPLS-AA for 3+ ions? How can I
> convert the parameters of Na and Ca from the opls to the standard gromacs
> force-field ? Please help me if you can :) Mira
> 

Dealing with transition metals is a complicated question.  See here:

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

I have no idea whether or not suitable parameters exist within OPLS-AA for any 
of these 3+ species.

Also realize that the task of "converting parameters" for Na+ and Ca2+ is not 
one you should undertake.  All Gromacs force fields, as far as I know, contain 
parameters for these two ions.  Thus you should not try to port any parameters 
from one force field to another, for reasons explained on the Parameterization 
page linked above.  Force fields should not be mixed or manipulated.  Further 
(just FYI), there is no such thing as a "standard Gromacs force field."  Please 
see the manual for the reasons why this statement is incorrect.

If you started your project with a Gromos96 force field, and are now realizing 
that OPLS-AA may be the better choice, you should start over, appreciating now 
that force field choice is something that should be researched in-depth before 
starting a project, not mid-stream.

-Justin


-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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