[gmx-users] Dihedral potential with chirality

[Mark Abraham]

On 31/01/2012 2:59 PM, Li SUN wrote:
> So please look at the attached figure which is exactly the leftmost 
> subfigure of Figure 4.8 from manual. Given one plane defined by 
> (j,k,l), the cases where <case1> i is above the plane and <case2> 
> below the plane can give the same dihedral angles.

Only if they are measured in a unsigned fashion.

> But chirality can distinguish the two cases: define chirality = ( (lk) 
> x (kj) ) . (ji), then chirality is positive for <case1> and negative 
> for <case2>. Am I right?

During the flipping process, the energy/force from the dihedral 
restraint potential will increase because the angle deviates from the 
programmed one. This will act to prevent flipping occurring without 
needing to trouble with computing a signed dihedral angle. If you pull 
too hard, then the restraint has insufficient effect. Choose wisely.

Mark

>
>
>
>
> On Mon, Jan 30, 2012 at 6:01 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 31/01/2012 11:53 AM, Li SUN wrote:
>>     Hello,
>>
>>     I am doing pulling simulations with GROMACS and would like to
>>     keep the chirality of the protein along the trajectory otherwise
>>     the protein will take the wrong chirality especially at long
>>     extensions. I have checked that using the improper dihedral or
>>     dihedral restraint can restrain the dihedral, but dihedral
>>     restraint is not equivalent to chirality restraint.
>
>     Why not? See 4.2.11 of manual and figure 4.8.
>
>     Mark
>
>
>>     So I am wondering if there is a "chirality restraint" somewhere
>>     in GROMACS. Otherwise I might have to modify the code...
>>
>>     Thanks in advance!
>>
>>
>>     -- 
>>     Li Sun
>>     Department of Physics
>>     University of California, San Diego
>>
>>
>
>
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>
>
> -- 
> Li Sun
> Department of Physics
> University of California, San Diego
>
>

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