[gmx-users] about intermolecular interactions

[Justin A. Lemkul]

wuxiao wrote:
> Dear GMXers,
>  
>   For long time, I have had a puzzle: while the top file generally 
> describe interactions in a molecule, intermolecular interactions are not 
> explicitly in the top file. How are these intermolecular interactions 
> described in GROMACS? Thanks a lot for any reply.

Since each atom is given a specific type, certain nonbonded parameters are 
associated with that type, per the specifications in the force field.  The 
method for calculating these interactions is also dependent upon the force field 
you're using.

-Justin

>   Sincerely,
>   Chaofu Wu, Dr.
> 
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-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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