[gmx-users] Request for dihedral PMF test system or complete alanine dipeptide topology file

Chris Neale chris.neale at utoronto.ca
Thu Apr 26 22:12:23 CEST 2007


>I have done similar calculation. Look at the supporting
>info for http://dx.doi.org/10.1021/jp068587c. If you find
>anything useful for you feel free to contact me.

Thanks Vojtech. I am going to try to repeat your Figure 2. If I can do that then I can confirm that there is some problem with my 
oplsaa topology and I can debug from there.



>Just out of curiousity, which GROMACS version are you using? The
>dihedral restraints were sort of broken in 3.3 originally; this is
>fixed in 3.3.1.

I use 3.3.1, thanks for checking.

>Right. I remember looking into this at one point, and I don't think
>the manual is correct; it looks to me like dihres.c handles
>periodicity properly. In particular, there is the followign comment in

It's good to see that this is actually a comment in the source code, I didn't look there.
Perhaps the manual should be updated?

>I assume you're clear on the fact that the phi and dphi are in degrees
>but the force constants aren't? And your units are otherwise correct?
>(i.e. you're remembering output is in kJ/mol?)

I use phi in degrees and always use dphi=0
For wham I convert my force constant to kcal/mol/deg^2 by multiplying the fc value like this:
# 500 kJ/mol/rad^2 * 1rad^2/3282.8063485deg^2 * 1kcal/4.184kJ= 0.0364026 kcal/mol/deg^2

>I can send you topologies if you want,

No, that's ok. I am actually convinced that my methodology is working and that there is some problem with my alanine dipeptide topology.
Thanks for all your help. I will post something again once I have resolved this problem.

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