[gmx-users] Re: Simulation with CsCl

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jun 9 16:21:29 CEST 2010

Dear Sonali,

Unfortunately development of force-field parameters is difficult, and
even more so for bivalent ions and transition metals. This is certainly
not suitable as a project to begin with.

Having said that, a careful search in the literature will reveal that
many sets of parameters for metal ions do exist. Try to find a set that
works best with the water model that you're using or your particular
model, and carry out some simulations to validate that the results are
correct, reproducible and robust. The following references discuss some
aspects of simulations of ions and proteins:

   Author = {Project, E. and Friedman, R. and Nachliel, E. and Gutman, M.},
   Title = {A Molecular Dynamics Study of the Effect of Ca{2+} Removal
on Calmodulin Structure},
   Journal = {Biophys. J.},
   Volume= {90},
   Pages = {3842-3850},
   Year = {2006}

author = "Fyta, M and Kalcher, I and Dzubiella, J and Vrbka, L and Netz,
R R",
title = {Ionic force field optimization based on single-ion and ion-pair
solvation properties},
journal = "J Chem Phys",
year = "2010",
volume = "132",
pages = "024911-024911"


sonali dhindwal wrote:
> Hello All ,
> I am also trying to simulate my protein with Mn ion present in it.
> So can I create the topology entry for Mn ion similar  to MG2+ ion ?
> and how can I get the values of C6 and C12 leonard jones potential in
> [atom type] entry and will it be required to add [nonbond_params] also
> ? how can I get them ?
> Also I want to use Fe2+ also, but it  is also not included in gromos
> force field. This problem of adding other ions and molecule in the
> system always remains. And being new to this field, can someone
> suggest in simple terms how to include these considering the person is
> not an expert in this field.
> Please help.
> --
> Sonali Dhindwal
> --- On *Tue, 8/6/10, Vitaly Chaban /<vvchaban at gmail.com>/* wrote:
>     From: Vitaly Chaban <vvchaban at gmail.com>
>     Subject: [gmx-users] Re: Simulation with CsCl
>     To: gmx-users at gromacs.org
>     Date: Tuesday, 8 June, 2010, 9:03 PM
>     > Hi all:
>     > I am trying to simulate a polysaccharide in solution of water
>     and CsCl, but
>     > cesium is not parametrized in the gromacs 4. I am using the force
>     > field GROMOS 96.
>     > I have looked for the parameters of Cs+ in the OPLS Force field
>     and I have
>     > created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I
>     have include
>     > the parameters for Cs+ in the "ions.itp" file, but it didn't
>     work, Can
>     > someone help me?
>     > Thanks in advance.
>     > Cecilia.
>     Cecilia -
>     You do not need so many files so cesium. Just copy your parameters to
>     the force field used and create the topology entry for cesium similar
>     to
>     [ moleculetype ]
>     Ar         1
>     [ atoms ]
>     1   Ar    1    Ar      Ar    0  0.0
>     Do not forget, cesium+ is an ion...
>     -- 
>     Dr. Vitaly Chaban
>     --
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.uzh.ch
Skype: ran.friedman

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