[gmx-users] get a box of 100 molecules

[Adrien Delmont]

--- On Wed, 3/11/09, Adrien Delmont <adriendelmont at yahoo.com> wrote:

From: Adrien Delmont <adriendelmont at yahoo.com>
Subject: Re: [gmx-users] get a box of 100 molecules
To: jalemkul at vt.edu
Date: Wednesday, March 11, 2009, 9:46 PM







The molecule I use is a simple hydrocarbon ( n-heptane ) and I think that I should add something like  dihedral, bond, angle parameters after I search the literature. I found some information about that. I think I will add parameters into the related force fields .itp file. Is it true ? And then I will create a box of 100 molecules without any error.

--- On Wed, 3/11/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] get a box of 100 molecules
To: adriendelmont at yahoo.com, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, March 11, 2009, 9:11 PM

Adrien Delmont wrote:
>  I just want to add missing parameters for my molecule in order to get
...gro and top files for example GROMOS96 43a2 force field . How can I add
missing parameters ? I didn't find any information about this procedure.
I'm waiting for your help.
>  

You'll have to define what you mean by "parameters" - is this
some new small molecule that has not been parameterized under this force field? 
Are you starting from scratch?  If so, this is not a trivial problem for a
beginner. Read here:

http://wiki.gromacs.org/index.php/Parameterization

If you have adequate parameters for most of your molecule and are missing
something like a dihedral, etc. then read the primary literature and derive it
yourself.  This process is also complicated, but is probably less work than
coming up with parameters for a brand new molecule.

-Justin

> Thanks in advance
> 
> 
> --- On *Wed, 3/11/09, Mark Abraham /<Mark.Abraham at anu.edu.au>/*
wrote:
> 
>     From: Mark Abraham <Mark.Abraham at anu.edu.au>
>     Subject: Re: [gmx-users] get a box of 100 molecules
>     To: "Discussion list for GROMACS users"
<gmx-users at gromacs.org>
>     Date: Wednesday, March 11, 2009, 4:58 PM
> 
>     Adrien Delmont wrote:
>     >     >     >
------------------------------------------------------------------------
>     > *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 ?
> 
>     You can't just mix force fields. See
>     http://wiki.gromacs.org/index.php/force_field
> 
>     Mark
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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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