Darrell Koskinen wrote:
Hi Tsjerk,
So then, if I understand correctly, setting "constraints = all-bonds" is
not as realistic as setting "constraints = none", since the latter will
allow for flexible (e.g. harmonic) behavoir which is more realistic than
fixing the bond to a certain distance, correct?
Actually not. It would be a better model of a harmonic potential (duh),
but it has been shown that the use of constraints can lead to a (more?)
acceptable model of a real system, and they allow a larger integration
time to boot. Check out the papers for the constraint algorithms (refs
in GROMACS manual).
Mark
Date: Wed, 11 Nov 2009 21:45:44 +0100
From: Tsjerk Wassenaar <tsje...@gmail.com>
Subject: Re: [gmx-users] Constraints & Restraints
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<8ff898150911111245u63c6aa65sa839f24634352...@mail.gmail.com>
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Hi Darrell,
Constraints and restraints also apply to relative positions. A bond
constraint fixes the bond to a certain distance. constraints =
all-bonds means that all bonds are to be converted to constraints,
rather than have them flexible, e.g. harmonic. Harmonic bonds are
actually more like restraints, penalizing deviations from the
equilibrium values. These equilibrium values and the 'penalty
function' are described in the force field.
Hope it helps,
Tsjerk
On Wed, Nov 11, 2009 at 9:32 PM, <darre...@ece.ubc.ca> wrote:
Hi,
I just have a quick question on contraints and restraints. My
understanding is that "constraints" fix the position of an atom in
space and "restraints" restrain the deviation of the atom's position
from its equilibrium point. Is that correct? If so, then I am a little
confused by the purpose of "constraints = all-bonds" or "constraints
= none" in an mdp file, since by selection of a force field, which has
bond/angle/dihedral stretching/bending/torsion constants, we are
specifying the constraints applied to the simulation. So then what is
the purpose of "constraints = all-bonds" and "constraints = none"?
Thanks.
Darrell
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