[gmx-users] Re: Re: angle restraints

[David Mobley]

Maarten,

So you are saying that lambda is just controlling the restraints and
nothing else? That is, you are using lambda-dependent angle
restraints? If this is the case, the problem is the "fix" for the bug
that I referred you, as implemented in 3.3.1. From the "bugzilla"
page, here's the fix:

>This was a nasty bug.
>The problem was that the angle-restraint parameters were stored
>incorrectly in the tpr file.
>I have fixed it completely in the CVS.
>I also made a fix for 3.3.1, but there the B-state parameters
>are always copied from the A-state.

In other words, in 3.3.1, the claim is that angle restraint parameters
can't be made to be lambda-dependent; B state and A state parameters
are the same. I am confused why you would be getting a nonzero
dv/dlambda at all in this case.

According to Berk, the angle restraints have the correct lambda
dependence in the CVS version. So if you are really intent on doing
things this way (that is, using lambda-dependent angle restraints) you
may want the CVS version.

Alternatively, you can do what I do, which is run simulations using
normal (non-lambda dependent) angle restraints with a bunch of
different spring constants, rather than using the free energy code.
Think of the spring constant like lambda. Then dV/dlambda=d(restraint
energy)/dK, where K is the spring constant. For harmonic restraints,
this is (restraint energy)/K. So you can compute dV/dlambda yourself
from the energies that are output by just taking the angle restraint
energy and dividing by the spring constant.

Again, I'm still not clear that this is exactly what you're trying to
do. As far as I can tell if your only lambda dependence is in the
angle restraints, and you are using 3.3.1, you should be getting a
dv/dlambda that is zero everywhere, unless you've done something
strange like turning on soft core potentials or something.

David


On 5/11/06, Maarten Wolf <maarten_wolf at yahoo.co.uk> wrote:
>
> David,
>
> Thanks for your reply.
>
> I am currently using 3.3.1 code.
>
> I am increase the force, to be able to calculate the free energy
> required of introducing the angle restraints in the system. I use small
> force increments each run, using a delta_lambda of 0.
>
> Decreasing or increasing in my view only changes the sign of the
> overall graph, but it should not allow dG/dl to cross zero.
>
> Thanks,
> Maarten
>
> > > From: "David Mobley" <dmobley at gmail.com>
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Date: Thu, 11 May 2006 09:34:28 -0700
> > Subject: Re: [gmx-users] angle restraints
> >
> > Maarten,
> >
> > What version of the code are you using? There was a bug in the angle
> > restraints code until 3.3.1 (or 3.3 cvs) which caused angle
> > restraints
> > to turn off gradually as a function of lambda in free energy
> > calculations, if I remember correctly. (See bugzilla for details:
> > http://bugzilla.gromacs.org/show_bug.cgi?id=43).
> >
> > However, I'm not sure that relates to the problem you're describing,
> > but it probably does, depending on the version you are using.
> >
> > What exactly are you changing in the free energy calculation? Are you
> > changing the angle restraint as a function of lambda? If so, which
> > way
> > are you changing it? Decreasing or increasing restraints?
> >
> > David
> >
> >
> >
> > On 5/11/06, Maarten Wolf <maarten_wolf at yahoo.co.uk> wrote:
> > > Dear users,
> > >
> > > I have a small system with a number of small peptides. I want to
> > > constraint the angle between the N-term to C-term vectors of
> > different
> > > peptides. This works well, but if I do a FEP calculation the dG/dl
> > > becomes smaller than zero at some point.
> > > I expected it to be at least allways greater than zero (zero in the
> > > limit that the restraint does not have to do anything), since a
> > force
> > > has to be aplied to restraint the angles.
> > > Can anybody explain where I am going wrong?
> > >
> > > Thanks
> > > Maarten
> > >
> > > Send instant messages to your online friends
> > http://uk.messenger.yahoo.com
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>
>
> MvG Maarten
>
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