[gmx-users] [ nonbonded_params ] and opls-aa

Berk Hess gmx3 at hotmail.com
Tue Mar 29 08:38:19 CEST 2005

>From: Paul Rowntree <Paul.Rowntree at USherbrooke.ca>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] [ nonbonded_params ] and opls-aa
>Date: Sun, 27 Mar 2005 01:41:59 -0500
>Greetings all;
>I am trying to add an LJ interaction to an opls-aa ff; my way of extending 
>ff is to include a small .itp file into the topology file, rather than
>modifying the distribution ff files.  In this file I define my types etc, 
>the LJ parameters.
>In the distribution ffoplsaa.itp file, the default combintaion rule is mode 
>requiring sigma and epsilon values.  The printd manual indicates that this
>convention will always be applied to the [nonbonded_params] inforamtion.
>However, when I do a gmxdump of the resulting .tpr file, I find a new 
>type in the LJ list that has exactly the same numerical values as my sigma
>epsilon pair, but the listing format implies they are being interpreted as 
>and C12 values, which would be MUCH more repulsive than intended.  The 
>results support this interpretation, and the run is clearly not behaving 
>It seems as if grompp has ignored the combination rule setting in the [ 
>] parameter block.
>So the question is : should I be able to include values in sigma epsilon 
>when I extend the opls-aa force field ?   I can recalculate the C6 and C12 
>course, but it takes away from the pure opls 'look and feel' of the 

This problem has already appeared (I think more than once) this month on the 
I have fixed it in CVS and for the next release.
For the moment you will have to enter C6 and C12.


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