[gmx-users] Re: angle restraints

Maarten Wolf maarten_wolf at yahoo.co.uk
Tue May 16 07:31:22 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.
I did this already and with gmxdump it returned all four parameters
(cpA, cpB, PhiA, PhiB) as input. But what I do not know is if these
parameters can be changed afterwards (perhaps in mdrun). I do not
expect this, but I am not sure it will not happen.

> 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 removed this fix, before implementing my own. If you are interested
you can find it on bugzilla or I can send it to you.

> > 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.
I do not understand this. 
Turning the restraints off is only affecting the highed of dG/dl and
turning it off means that you slowly go to zero.


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