[gmx-users] get a box of 100 molecules

[Adrien Delmont]

________________________________
From: Adrien Delmont <adriendelmont at yahoo.com>
To: jalemkul at vt.edu
Sent: Wednesday, March 11, 2009 6:09:53 PM
Subject: Re: [gmx-users] get a box of 100 molecules


I didn't get gro and top files with any force field in Gromacs. I basicly want to use oplsaa and GROMOS96 43a2 force field (improved alkane dihedrals) . I think I should add all the parameters but  how can I add my parametes both into oplsaa and GROMOS96 43a2 force field ?

Thanks in advance






________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, March 11, 2009 5:48:59 PM
Subject: Re: [gmx-users] get a box of 100 molecules



Adrien Delmont wrote:
> /Dear Users,
> 
> I'm new to Gromacs. Before I try to generate a box of 100 molecules, I wanted to ask it to the users. Can I get a box of 100 molecules that are randomly //distributed/ /and not attached to each other using the commands below? If there are something wrong in commands please share your valuable suggestions with me.  

Try it and see.

> Thanks in advance
> ///
> Adrien
> 
> pdb2gmx -f mol.pdb -o mol.gro -p mol.top -i mol.itp ( then chose suitable force field )
> ////

This will only work if the force field contains parameters for your molecule.

-Justin

> //////////genbox////////// //////////-ci////////// mol.gro //////////-nmol 100//////// //-o 100mol.gro //////-p
>  100mol.top//// ////////-box 12 12 12//////////
> 
> //
> 
> 
> 
> ------------------------------------------------------------------------
> 
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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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