Subject: Re: CCL:addiong ions to simulation box

From: "Mgr. Lubos Vrbka" <lubos.vrbka=at=uochb.cas.cz>
Date: Sat, 05 Mar 2005 10:25:08 +0100

hi stefano,

thank you for your hint with gromacs... however it seems that it is 
seriously broken in this respect. see, e.g.
http://www.gromacs.org/pipermail/gmx-users/2004-August/011925.html
i always encounter the same problem - when larger amount of molecules is 
being added to simulation box with protein, genbox starts placing the 
molecules inside the protein structure... it's a pity, since this is 
exactly the functionality i need... :(

if you have any other suggestions, please let me know.

regards,
lubos

-- 
.....................................................
Mgr. Lubos Vrbka

Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
.....................................................

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From: David van der Spoel <spoel :: xray.bmc.uu.se>
Date: Sat, 05 Mar 2005 11:53:50 +0100

> exactly the functionality i need... :(

The example in the mailing list is quite extreme in the sense that they
try to add 2400 molecules to a 4 x 4 x 4 nm box. I'm not sure how broken
it is. An alternative is to solvate a protein in a mixed solvent (using
genbox) or simply build a box with lots of space between molecules and
then use pressure scaling MD to compress the box.

-- 
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 :: xray.bmc.uu.se    spoel :: gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

-- 
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 :: xray.bmc.uu.se    spoel :: gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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From: forli * unisi.it
Date: Sat, 05 Mar 2005 14:09:01 +0200 (MET-DST)

hi, Lubos,

> molecules inside the protein structure... 

how you can easily imagine, number of molecules and volume of the box
are essential, because apparently the first parameter drive the
placement of solvent in to the box. I agree with David, the algorithm is
not perfect, of course, so using large box with a lot of mols, it can
fails, but fine tuning parameters leads me to really good results.
I don't yet tryed the pressure gradient, but I think it's an elegant way
to test as soon as possible

Stefano

--

***********************************
 Stefano Forli
 Dip. Farmaco Chimico Tecnologico  
 Universita' degli Studi di Siena  
 Via Aldo Moro                    
 I-53100 Siena, Italy              
 Phone: ++39 0577 234307      
 Fax: ++39 0577 234333   
 e-mail: forli * unisi.it
***********************************

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From: Arvydas Tamulis <tamulis.-at-.mserv.itpa.lt>
Date: Sat, 5 Mar 2005 19:02:20 +0200 (EET)

Hello Mgr. Lubos Vrbka,

We put many water and lipid molecules surrounding 
PNA+Sensitizer::LipidPrecursor self-assembling system
by using Molden software and later doing PM3 geometry optimization
using G03 or GAMESS packages.

Regards,
Arvydas Tamulis

On Fri, 4 Mar 2005, Mgr. Lubos Vrbka wrote:

> Hello everybody:
>
> Is anyone aware of software allowing replacing waters in the simulations cell 
> (protein + water box) by small molecules? "Automatic" solution is preferred, 
> since I need to put many molecules to the solution.
>
> Any help is highly appreciated. With best regards,
> Lubos
>
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