[gmx-users] Dihedral potential with chirality

[David van der Spoel]

On 2012-01-31 19:49, Li SUN wrote:
> Thanks for the explanation! Is the improper dihedral in GROMACS
> implemented in an unsigned fashion?
>
Yes, that means that changing the order of atoms changes the sign and 
this may give you the opposite chirality.
>
>
> On Mon, Jan 30, 2012 at 9:01 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     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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>
>
> --
> Li Sun
> Department of Physics
> University of California, San Diego
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se