[gmx-users] Dihedral potential with chirality
Mark.Abraham at anu.edu.au
Tue Jan 31 06:01:33 CET 2012
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.
> 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:
>> 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.
>> 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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