Justin,
I appreciate your helpful reply. To summarize the additional points I
make below:
(1) the code is right as far as calculating the dihedral restraint
potentials, but the manual has a bug, and
(2) the settings for dihedral restraints should be documented,
preferably in the wiki, which I'm not able to edit.
Justin wrote:
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;
Thanks for pointing that out. As I look closer, I also see
if (dp dphi)
ddp = dp-dphi;
else if (dp -dphi)
ddp = dp+dphi;
else
ddp = 0;
followed by
vtot += 0.5*kfac*ddp*ddp;
Your code snippet indicates that the code is correct (absolute value
of dp when calculating the angle modulus) and mine also indicates that
the code is correct (absolute value of dp when calculating the
restraint energy).
The manual, however, should have absolute values in each place that
phi-phi0 appears. How can the manual be corrected expending the least
effort?
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 ajakal type label phi dphi kfac power
57 915 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.
snip
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.
So then it seems there are two ways to set force constants -- by
setting dihre_fc in the mdp file and by setting kfac in the dihedral
restraints itp file. Good to know.
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.
For now I'll just cross my fingers and put a 2 ... but it would be
good for all of these doohickeys to be documented.
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.
sniip
I might get around to updating this page with the above information, unless
there is more information to be considered, or I'm wrong :)
I don't appear to have the appropriate privileges for editing, but
that's okay, as it seems like a lot of responsibility.
Have fun,
Dan
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
