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

mernst at tricity.wsu.edu mernst at tricity.wsu.edu
Thu Feb 2 22:33:31 CET 2006

> 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.
>>Thank you for the hint. I was able to fix the zeros in the bonds, but I am
>>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.

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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