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.abra...@anu.edu.au
<mailto:mark.abra...@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.abra...@anu.edu.au <mailto:mark.abra...@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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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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