[gmx-users] Re: angle restraints

David Mobley dmobley at gmail.com
Mon May 15 19:07:31 CEST 2006


> 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.

Are you sure this worked properly? I tried to do this myself at one
point and couldn't find the bug that was causing the problem.

To check it, you should gmxdump your tpr file and look for the cpA,
cpB, etc parameters for the angle restraint in question. Every time I
did it, one of these was zero.

Also, if you are using 3.3.1, you would need to modify the angle
restraints code to *use* these parameters again, since as I mentioned
before, the "fix" in 3.3.1 was to make angle restraints always use the
A state parameters.

> 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.

I don't think there are any other bugs; I've used this code a lot now.
But it's possible. You could try computing something where you know
what the answer should be.

It could cross zero if your angle restraints were turning off, I think.


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