[gmx-users] get a box of 100 molecules

Adrien Delmont adriendelmont at yahoo.com
Wed Mar 11 23:12:19 CET 2009 

If I create an .rtp file for my molecule how can I use this file when I producing gro and top files and Can I use this .rtp file with oplsaa and gromos 96 force fields for two different md run successfuly ? Because I plan to run md simulations for all atom and united atom force fields and compare the results. Secondly If I use PRODRG , the only force field I can use is oplsaa. Is it true ? Can't I use a gromos 96 force field ?

--- 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: "Gromacs Users' List" <gmx-users at gromacs.org>
Date: Wednesday, March 11, 2009, 9:53 PM


Adrien Delmont wrote:
> 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.
> 

Most (if not all) of the parameters you will need will already be present in
the force field.  No modification of any of these files should be necessary..  If
you want to use pdb2gmx to create your topology, you need to create an .rtp
entry. For a simple alkane (especially with a UA representation), it should be
trivial to write the topology by hand with a text editor and a thorough
understanding of Chapter 5.

Alternate ideas:

1. Use PRODRG to generate a rough topology. Verify its contents before
proceeding, make any modifications you need, and validate the resulting
topology.
2. Don't use Gromos96.  AFAIK, none of the Gromos variants deal very well
with hydrocarbon chains.  OPLS might be better, but I think there are some
limitations there, too.

-Justin

> --- 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
> 
>     ========================================
> 
> 

-- ========================================

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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