[gmx-users] get a box of 100 molecules
Adrien Delmont
adriendelmont at yahoo.com
Fri Mar 13 15:47:16 CET 2009
What are the suitable options for Chirality , Full charges , Energy
Minimization in PRODRG to get input files for hydrocarbon molecules ?
And If I choose Full charges : YES , I will get the files that include
charge info. Can I erase the charge info and write the charge info I
got from Gaussian ( net charge is zero ) according to the order of
atoms that I paste to the PRODRG screen ? Could you give me some
advices about this ?
Thanks in advance
Adrien
________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: adriendelmont at yahoo.com; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, March 12, 2009 12:17:57 AM
Subject: Re: [gmx-users] get a box of 100 molecules
Adrien Delmont wrote:
> 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 ?
>
I think you should start by reading the manual about .rtp files and how they are used. Each force field has its own .rtp, so no, you cannot use the same .rtp file with different force fields. Make a local copy (in your working directory) if you choose to modify your .rtp files; if you are unsure of what you are doing you can seriously screw things up.
PRODRG produces Gromos-compatible force fields, not OPLS; this is answered in the FAQ at the PRODRG site.
I reiterate: read the manual, be comfortable with how the file types are used, then proceed.
-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: "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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> > > > > >
> ------------------------------------------------------------------------
> > > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
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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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>
>
> ------------------------------------------------------------------------
>
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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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