[gmx-users] Two [ dihedrals ] Sections in Topology

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi
> 
> After pdb2gmx I got two [ dihedrals ] sections in the topology file. 
> 
> 
> [ dihedrals ]
>   ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
>     2     1    19     8     5
>     6     8     9    10     5
>     6     8    19     1     5
> 
> [ dihedrals ]
>   ai    aj    ak    al funct            c0            c1            c2            c3
>    1     8     6     4     2    180   100
>    1     2     4     5     2    180   100
>    1    10    11    13     2    180   100
> 
> 
> Why is pdb2gmx doing this? I commented the first block out. Is this allowed?
> 

You can comment anything out that you like, but if you don't know what you're 
doing you're likely to completely break the physical model.  Note the function 
types (which are explained in the manual).  The first directive indicates 
Fourier dihedrals (a type of proper dihedral) while the second indicates 
improper dihedrals.

-Justin

-- 
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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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