[gmx-users] Re: gromacs
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 30 14:25:42 CEST 2010
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:
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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