Ok, I can update this situation (see below quote):
On 18/10/10 03:30, Mark Abraham wrote:
And then, I read on the Gromacs website *this*
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
" 2. The manual is a bit unclear about whether this type of
dihedral restraint is stable for use near 180 degrees. Chris
Neale has found that everything appears to behave normally and
as expected over the entire range of dihedral angles including
180 degrees. However, one must avoid the situation in which the
actual dihedral is close to 180deg away from the restrained dihedral."
And I know that somehow the potential is discontinuous and/or
anyway not intended to be well-behaved everywhere:
http://www.mail-archive.com/[email protected]/msg12353.html
"> On Tue, Feb 26, 2008 at 11:37 AM, David Mobley<[EMAIL
PROTECTED]> wrote:
The other way of putting what Mark said is that phi is
only meaningful on some range (-pi to pi, or 0 to 2pi, depending
on how you define it)
and so what you require is that the potential be
harmonic for the
region in which phi is meaningful. You don't care what
happens outside that. Or, in this case, you handle the issue by
mapping phi values outside the allowed range back into
that allowed range."
(I don't get what does it mean to "map back" phi values, by the way).
I am no MD expert, so maybe my hypothesis is totally off, but I
am reasonably sure that either I do not understand correctly how
dihedral restraints work, or I am suffering by the discontinuity
of the way the potential is implemented (Or both). I would like
to know:
I managed to patch the dihedral restraining part so to mitigate the
issue. The problem lied in the 180-degrees discontinuity in the force,
where it jumps from a highly positive to a highly negative value, like
(Y=force, X=angle):
/|
/ |
/ | /
/ | /
|/
I have cut the ends close to the phi=180 and "connected" the force
values like that:
/\
/ \ /
/ \ /
\/
and then redefined the energy to be the integral of that line.
This way it works -you can have decent restraining along all phi angles
without risking to freeze, provided the energy barrier at 180 is not too
high.
The patch looks really ugly -it has been kludged in quite a hurry and...
well, looks obscene, but if someone wants to look at it, let me know!
m.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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