[gmx-users] on force fields

[Mr Bernard Ramos]

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. 

--- 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>/* wrote:
> 
> 
>     From: Mark Abraham <Mark.Abraham at anu.edu.au>
>     Subject: Re: [gmx-users] on force fields
>     To: "Discussion list for GROMACS users" <gmx-users at 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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