[gmx-users] Re: angle restraints

Maarten Wolf maarten_wolf at yahoo.co.uk
Mon May 15 11:06:55 CEST 2006 

>From: "David Mobley" <dmobley at gmail.com>
>Date: Fri, 12 May 2006 10:05:55 -0700
>Subject: Re: [gmx-users] Re: Re: angle restraints
>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:

yes, and I fixed it already.

>>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.

Correct, but I made some changes to ensure correct storing of values in the tpr file. Correct me if I am wrong, but the storage of these values only occurs during the generation of a tpr file with grompp.
 
I am not sure if there are other bugs in the angle restraints value. If so this might explain why the dG/dl crosses zero. I do not understand it otherwise.

>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.
 
Thanks, I will try this as well. It should be sufficient for my goal.

>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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