[gmx-users] on force fields

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 21 03:41:26 CET 2011

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:


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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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