[gmx-users] [pairs] and [dihedrals]

[Justin A. Lemkul]

you zou wrote:
> Hi everyone,
> 
> I have one question about topology, If I want to write topology by hand, 
> how can I write pairs and dihedrals without mistakes? Is there any free 
> softwares to use?
> 

If you're using some automated program, then you're not doing it by hand :) 
There are several on the Gromacs' User Contribution site.  There is no 
substitute for understanding the intrinsics of your desired force field and how 
it treats these terms, as well as Chapter 5 of the Gromacs manual. 
Understanding all of this is the only way to not make mistakes (being careful of 
course to properly implement all that you have learned from your reading).

-Justin

> Thank you
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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