Daniel L. Ensign wrote:
Hello gmx-users, you rock and rollers,
Equations 4.74 and 4.75 in my copy of the manual have (please pardon my
pseudo-LaTeX):
(4.74)
\phi' = (\phi - \phi_0) MOD 2\pi
(4.75)
V(\phi') = \frac{1}{2}k ( \phi' - \phi_0 - \Delta \phi )^2 if \phi' >
\Delta \phi
or
V(\phi') = 0 if \phi' \leq \Delta \phi
but should there be absolute values around all of the \phi-\phi_0? Which
way is it in the code -- with the absolute distance between \phi and
\phi_0 or the directed distance?
It looks like absolute values are considered. From src/gmxlib/dihres.c:
/* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
* force changes if we just apply a normal harmonic.
* Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
* This means we will never have the periodicity problem, unless
* the dihedral is Pi away from phiO, which is very unlikely due to
* the potential.
*/
dp = phi-phi0;
if (fabs(dp) > dphi) {
/* dp cannot be outside (-2*pi,2*pi) */
if (dp >= M_PI)
dp -= 2*M_PI;
else if(dp < -M_PI)
dp += 2*M_PI;
Also, as far as I can tell (and some mornings I definitely don't read
too good) neither the manual nor
http://wiki.gromacs.org/index.php/Dihedral_Restraints define the fields
in [ dihedral_restraints ], although the latter does name them. There, I
see
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
5 7 9 15 1 1 180 0 1 2
ai, aj, ak, al = atom numbers, obviously
type = ?, but I'm guessing there's only one type anyway
Probably so.
label = what is this one?
Looks to be bookkeeping. The code doesn't seem to use it other than to print
debug information, but I could be wrong since I haven't surfed around it very long.
phi means phi0 ?
Yes.
dphi means Delta phi, I guess
Yes.
kfac is the force constant, probably
Indirectly. This term is equivalent to the fac value in distance restraints.
Since the force constant is specified in the .mdp file, different restraints
would otherwise have to be restrained with equivalent force constants. The
value of kfac is multiplied by the value of dihre_fc in the .mdp file, so that
different restraints could have different force constants.
power = what is this one? Does 2 give me harmonic constraints?
Not a clue on this one. Also doesn't seem to be used in the code, but maybe
it's somewhere outside of dihres.c.
I'd be happy to translate any answers given to the wiki, assuming I get
answered and that I'm allowed to edit the wiki.
The wiki link you posted above doesn't actually exist any more, and actually
points to an empty page, even though the content is still online:
http://www.gromacs.org/index.php?title=Documentation/How-tos/Dihedral_Restraints
The old wiki doesn't actually exist, but has been merged into the Gromacs site,
so if you register as a user you can make contributions. If you have troubles,
I might get around to updating this page with the above information, unless
there is more information to be considered, or I'm wrong :)
-Justin
May the Force be with you (as long as it's calculated in hand-tuned
assembly loops),
Dan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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