[gmx-users] on force fields

[Justin A. Lemkul]

Mr Bernard Ramos wrote:
> Thank you, sir. That's nice of Gromacs to automatically assign new atom 
> types from an input pdb file. I check out the link as well.
> 

To be clear, an atomtype is only assigned if:

1. it is present in the .atp
2. it has relevant parameters assigned in ffnonbonded.itp (and possibly 
ffbonded.itp if it is involved in bonded interactions, as well)
3. it is utilized in a building block defined in the .rtp file, and
4. an atom with a name corresponding to that of the .rtp entry is found in the 
input coordinate file

All conditions must be satisfied for the resulting topology to be useful (or 
produced at all, for that matter).

-Justin

> --- On *Mon, 2/21/11, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] on force fields
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Monday, February 21, 2011, 10:41 AM
> 
> 
> 
>     Mr Bernard Ramos wrote:
>      > Thanks for the reply on my first querry. I have another one. If I
>     add a NEW atom type in *.atp file, will Gromacs automatically
>     recognize this atom type?   
> 
>     Theoretically, yes, provided that you supply any corresponding
>     parameters in, e.g., ffnonbonded.itp and ffbonded.itp.  However,
>     there is an unresolved bug related to atomtype assignment that may
>     be relevant:
> 
>     http://redmine.gromacs.org/issues/618
> 
>     It seems to me that any alterations to the .atp file cause things to
>     break down, so do not be surprised if there are problems.
> 
>     -Justin
> 
>      > Thanks.
>      >
>      >
>      > --- On *Wed, 2/16/11, Mark Abraham /<Mark.Abraham at anu.edu.au
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=Mark.Abraham@anu.edu.au>>/*
>     wrote:
>      >
>      >
>      >     From: Mark Abraham <Mark.Abraham at anu.edu.au
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=Mark.Abraham@anu.edu.au>>
>      >     Subject: Re: [gmx-users] on force fields
>      >     To: "Discussion list for GROMACS users"
>     <gmx-users at gromacs.org
>     <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >     Date: Wednesday, February 16, 2011, 1:53 PM
>      >
>      >     On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:
>      >>     Hi everyone!
>      >>          I need to update the gromos force field 53A6 with the
>     new force
>      >>     field 53ACARBO (JCC 10 NOV 2010).
>      >>          1. I will have to change the parameter values in the file
>      >>     ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are
>     these
>      >>     the only files that I need to update if I need to switch to
>     a new
>      >>     force field?
>      >>
>      >
>      >     You should make a copy of the whole force field directory
>     into your
>      >     working directory, rename the new directory suitably, make a
>      >     suitable change to forcefield.doc, and then edit .itp files
>      >     suitably. This means you're leaving your reference version
>     untouched
>      >     and can edit locally to your heart's content, and can be sure
>     you're
>      >     selecting the right force field with pdb2gmx and/or in your
>     .top file.
>      >
>      >>          2. The new force field 53ACARBO has a new gromos
>     functional form
>      >>     for select torsional potentials. How to I go over implementing
>      >>     this in gromos?
>      >>
>      >
>      >     Preferably as a sum of existing functional forms. Or use
>     tabulated
>      >     bonded interactions (see manual and wiki).
>      >
>      >     Mark
>      >
>      >     -----Inline Attachment Follows-----
>      >
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> 
>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================