Pawan Kumar wrote:
Hi,

You should add 14 cl ions.

Why 14? The number of Cl- ions that are necessary is pretty much spelled out by grompp, and the net charge of the system is printed in the .top (qtot section in [atoms]). If your system has a net charge of +2, add 2 Cl- ions, and so forth.

-Justin


Regards,
Pawan

On Mon, Apr 6, 2009 at 12:26 PM, akalabya bissoyi <bissoyi.akala...@gmail.com <mailto:bissoyi.akala...@gmail.com>> wrote:

    hello gromacs
    i am trying to minimise my protein-ligand complex in gromacs.but it
    shows that system has non zero charge
    can any body says how much *cl ion*, i have to add to neutralised
    it. i am terminal window text.
    thank u
-- AKALABYA BISSOYI
    N.I.T.Rourkela

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--
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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