[gmx-users] Dihedral potential with chirality

[Li SUN]

Thanks for the explanation! Is the improper dihedral in GROMACS implemented
in an unsigned fashion?



On Mon, Jan 30, 2012 at 9:01 PM, Mark Abraham <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>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
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