[gmx-users] generating conf.gro

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Aug 18 10:43:53 CEST 2008

Hi Vitaly,

Do you have a rather fixed ratio between the two? ion:solvent = 1:10
e.g. Then you could make an arrangement of a single ion with
surrounding solvent and replicate that with genconf. You could even do
a short simulation setting rvdw to less than half the size of your
small box :p for a bit of equilibration.



On Mon, Aug 18, 2008 at 10:29 AM, Vitaly Chaban
<chaban at univer.kharkov.ua> wrote:
> Hi,
> I want to create a system (conf.gro) consisting of a solvent and
> polyatomic (brachiated enough) ions.
> Using genconf and genbox I increase the number of molecules and then
> ions (or contrariwise). But genbox refuses to add all the requested
> particles at once (because of intersections, I guess). What I do? - I
> add the number of ions it allows and make short md run. Then a few
> other particles can be added. Repeating the procedure several times,
> the system is ready.
> The question is how to avoid these tricks? How to initialize the
> system at once (even with intersections). Further, the energy
> minimization will be done before MD itself. Of course, by means of
> standard gromacs tools.
> Thanks.
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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