[gmx-users] Changing Ionic strength in gromacs

[David van der Spoel]

On Wed, 2004-11-24 at 14:23 +0000, Miguel Machuqueiro wrote:
> Hi all,
> 
> I'm posting this message for a 2nd time hoping that someone (developers!!!) 
> can give me a hint.
> 
> I would like to know how Gromacs calculates the Ionic Strength of my system 
> (protein + solv + ions)?
> 
> The manual only refers to the Generalized-Reaction-Field and mentions:
> 
> "The ionic strength is computed from the number of charged (i.e. with non 
> zero charge) charge groups"
> 
> Running a small MD and checking the output, it shows:  I = 0
> 
> It seams to me that with or without counterions, Gromacs is setting the 
> Ionic Strength and kappa to zero, is this correct?
check the source in src/mdlib/force.c

> 
> Thank you,
> 
> =========================================
> Miguel Machuqueiro
> ITQB-Instituto de Tecnologia Química e Biológica
>      Universidade Nova de Lisboa
> Molecular Simulation Group - 6º Floor (Room 601)
> Av. da República, EAN, Apartado 127
> 2781-901 Oeiras, Portugal
> Tel. : +351 214469618 /Mobile: +351 96 7562285
> E-mail1: machuque at itqb.unl.pt
> E-mail2: masm at fc.ul.pt
> __________________________________________
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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