[gmx-users] generating conf.gro

Vitaly Chaban chaban at univer.kharkov.ua
Mon Aug 18 21:07:26 CEST 2008

Hi Tsjerk,

Thank you for this suggestion. It's a good idea to have previously
equilibrated bricks then used for a main system.

Unfortunately, my the ratios between ion and solvent usually appear
quite far from the integer because I have fixed concentration.
Moreover, a CNT is present in the same system... :)  The replication
will not simplify the procedure in the present case.

Does anybody have more ideas how to force all particles to be inserted
without consecutive equilibrations? I tried to reduce -vdwd of the
genbox but telling the truth, no difference was found (version 3.3.1).


2008/8/18 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> 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.
> Cheers,
> Tsjerk
> 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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