[gmx-users] Which is the real function used in computation?

Erik Lindahl lindahl at sbc.su.se
Thu Dec 22 10:45:56 CET 2005


On Dec 22, 2005, at 10:37 AM, 主月 :) wrote:

> Hi everyone:
>   From manual 3.2 chapter 4, i found there are many function for  
> non-bonded or bonded interaction. The function used in my  
> computation can be choosen by modify *.top.But the function has  
> already been set if we choose the force field.
>   For example, the Bond stretch function have Harmonic potential  
> and Fourth power potential. I choose gromos96 force field when i  
> used pdb2gmx to build molecule then it will choose Fourth power  
> potential. Then i modify the *.top to set function to 1 that is  
> Harmonic potential.Which is the real function used in computation?

The selection in your topology.

However, most force fields have only been developed/parametrized/ 
tested with their own choice of interactions. Unless you really know  
what you are doing it is not a good idea to change it (read: you will  
need to explain it to the referees).



Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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