[gmx-users] "B" state for free energy corrupts minimization?

David Mobley dmobley at gmail.com
Fri Feb 3 03:51:28 CET 2006

If the problem is what Berk thinks it is, a way to identify the
problem might be to set up a topology with only an A state. But make
the A state be the B state you're currently trying to use (that is,
set up a separate calculation for only the B endpoint). If you're
missing some parameters it should warn you that they're not found and
tell you which ones.


On 2/2/06, mernst at tricity.wsu.edu <mernst at tricity.wsu.edu> wrote:
> > Date: Thu, 02 Feb 2006 09:15:16 +0100
> > From: "Berk Hess" <gmx3 at hotmail.com>
> > Subject: RE: [gmx-users] "B" state for free energy corrupts
> >       minimization?
> > To: gmx-users at gromacs.org
> > Message-ID: <BAY110-F105B00ABA605C6586313A8E0A0 at phx.gbl>
> > Content-Type: text/plain; format=flowed
> >
> >
> >
> >
> >>From: mernst at tricity.wsu.edu
> >>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>To: gmx-users at gromacs.org
> >>Subject: [gmx-users] "B" state for free energy corrupts minimization?
> >>Date: Wed, 1 Feb 2006 23:46:45 -0800 (PST)
> >>
> >> >Indeed the zeros in the bonds (and probably also in the angles?) are the
> >> >problem.
> >> >This is caused by a bug that I have fixed in November,
> >> >but we did not release 3.3.1 yet:
> >> >http://www.gromacs.org/pipermail/gmx-revision/2005-November/000117.html
> >> >
> >> >Apparently some bonded interaction parameters are not defined
> >> >for bonded interactions that involve your 36 atom type in the B-state.
> >> >
> >> >You should add parameters for these bonded interactions,
> >> >either directly after the definition of the bonded interaction,
> >> >or in the force-field bondtypes and angletypes sections.
> >> >
> >> >Berk.
> >>
> >>Berk,
> >>
> >>Thank you for the hint. I was able to fix the zeros in the bonds, but I am
> >>having
> >>trouble tracking down the source of the zeros in the angles. Which file or
> >>files needed
> >>modification to fix this bug? I have been using 3.3. I tried downloading
> >>the source and
> >>building from CVS, but it failed:
> >
> > I would not try to change the source code, or use the CVS source.
> > The fix in CVS would produce the tpr file you want,
> > but it does not fix the actual source of the problem,
> > which is that you do not have parameters in the forcefield
> > for some bonded interactions in the B-state.
> >
> > You a probably only missing one or two angle parameters
> > in the forcefield.
> > You should look in the ff...bon.itp file for your forcefield.
> > Go to the angletypes section and copy the lines for
> > the original atomtype and replace the original atomtype
> > in the copy by 36.
> >
> > Berk.
> Berk,
> I know it should be fixable by attempting to duplicate one of a few possible parameters
> under different atom names, but so far I have been unable to do so. I probably have a
> blind spot from working on the same problem so long. I was hoping to use the CVS code so
> that the issued warnings would tell me which triplet of atoms did not have angles
> defined in the "B" state. I am altering more than the one nitrogen in the full case, and
> it would be very helpful to have output telling me what I still need to supply. I am
> starting to suspect that my last software package "magically" filled in some information
> for B-states that I need to make explicit in Gromacs, which is why I need to supply more
> non-standard parameters than I expected.
> Matt Ernst
> Washington State University
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