[gmx-users] the force field in GMX(further)

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 21 12:51:18 CET 2005

主月 :) wrote:
> Hi:
> In manual-3.2 chapter4 ,it said that the potential functions can be 
> subdivided into Non-bonded, Bonded and Special. Each of them has many 
> function. Can i choose any one of them just by modify funct in top file? 
> And when i use different type of force field?
> For example:
> In GROMOS96 53a6 force field ,i set bonds in top like follows :
> [ bonds ]
>     1     2     2 (3)
> that means it will use Fourth power potential for bond stretching 
> computation?
> if i want it use Morse potential bond stretching, i can do that just by 
> change the last column from 2 to 3?! Is that right? How can i get the ID 
> for each function?
yes and no. you still need parameters for the Morse function and none 
of the standard force fields has that, meaning you'll have to provie 
them yourselves. there also is an mdp option to convert harmonic bonds 
to Morse, rather crude, but functional.
> 3X all!
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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