Vojtech.:
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.
####
David:
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
dihres.c:
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.
Chris.
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