[gmx-users] a question about force fields

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 19 10:57:43 CET 2012

On 19/02/2012 7:26 PM, Banafsheh Mehrazma wrote:
> Dear Mark
> Thanks for your reply
> You said "These should function the same", are results of parm 99 and 
> amber 99 the same?
> Please explain more about (but you should check yourself that each 
> cites the same literature).

Random files that you find with software implement some model that was 
hopefully published somewhere. If those files (or the associated 
documentation) each claim the same published source, then you have 
grounds for knowing they're the same. Some random person on the internet 
telling you they're the same is next to useless :-)

> One more thing, I want to transfer Force Constant K? (kcal/ mol rad2) 
> and Equilibrium Bond Angle ?eq (º) from PARM99 TO AMBER99, however 
> there are no such factors in ffbonded.itp in ffamber99, I looked 
> through chapter 4, but didn't get any clue of what I should do.

Chapter 4 explains the function types and chapter 5 explains the file 
formats. You'll need to understand the relevant parts of both, and get 
the unit conversion right (chapter 2). And do a bunch of GROMACS 
tutorial material before even thinking about modifying force fields. :-)


> Best regards.
> Banafsheh
> On Sat, Feb 18, 2012 at 5:11 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 18/02/2012 7:23 PM, Banafsheh Mehrazma wrote:
>         Dear all;
>         I am wondering if the amber99 in gromacs package is the same
>         as PARM99
>         in Amber package, so that I can use the new modified
>         parameters (which
>         is made in Amber package) in my simulation in gromacs? Or should I
>         make some changes?
>     These should function the same - but you should check yourself
>     that each cites the same literature.
>     Mark
>     -- 
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