[gmx-users] The trouble with dihedral restraints: frozen peptide backbones
devicerandom at gmail.com
Tue Nov 23 17:02:32 CET 2010
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*
>> " 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:
>> "> 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
/ | /
/ | /
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
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!
Massimo Sandal, Ph.D.
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