[gmx-users] Protein angles / single point calculations

Matthias Ernst Matthias.Ernst2 at student.kit.edu
Thu Jan 12 11:14:14 CET 2012


I have some questions.
First, what dihedral angles will Gromacs produce and use in topology 
when simulating proteins? To be more specific, I was looking for psi 
(N-C(a)-C-N) and phi (C-N-C(a)-C) angles in all the dihedrals that were 
generated by pdb2gmx. I only found the psi angles but not phi. Is that 
by purpose?
Second, for testing purposes, I want to do single point energy 
calculations in vacuo with no cutoffs at given coordinates. When I use 
an mdp like the one below, it always changes the coordinates slightly 
but enough to change the energy values noticeably. Is there a better way 
to to this?
Third, I'm not sure if the coordinates are used correctly. To compare 
the energy values, I inserted a little piece of code in the energy 
evaluation routines which outputs the coordinates of all atoms. It seems 
that everything beyond the three digits after the decimal sign in the 
.gro files is filled with arbitrary numbers. I know that using floating 
point data types results in a loss of accuracy but I thought even with 
single precision, the accuracy should be higher than three digits?

Here is my mdp:
constraints   =       all-bonds
integrator    =       MD
nsteps          =       0
nstcomm     =       1
ns_type        =       grid
rlist              =       0.0
rcoulomb     =       0.0
rvdw            =       0.0
Tcoupl          =       no
Pcoupl         =       no
gen_vel        =       no
pbc              =       no

I would greatly appreciate any help and comments.

Best regards,
Matthias Ernst

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